US7794977B2

US7794977B2 - Means and methods for regulating gene expression

Info

Publication number: US7794977B2
Application number: US11/888,568
Authority: US
Inventors: Arie P. Otte; Arthur L. Kruckeberg; David P. E. Satijn
Original assignee: Chromagenics BV
Current assignee: Chromagenics BV
Priority date: 2002-06-14
Filing date: 2007-07-31
Publication date: 2010-09-14
Also published as: AU2003243059A8; US20080131930A1; WO2003106674A2; AU2003243059A1; US20050214906A1; US20080206813A1; WO2003106674A3; US7267965B2; EP1513936A2

Abstract

The invention relates to means and methods for regulating gene expression and production of proteinaceous molecules. The invention provides a method for producing a proteinaceous molecule in a cell comprising selecting a cell for its suitability for producing the proteinaceous molecule, providing a nucleic acid encoding the proteinaceous molecule with a nucleic acid comprising a STAR (STabilizing Anti-Repression) sequence, expressing the resulting nucleic acid in the cell and collecting the proteinaceous molecule. Providing at least one STAR sequence to a nucleic acid encoding a proteinaceous molecule will enhance production (yield) of the proteinaceous molecule by a host cell, increase the proportion of host cells with acceptable expression levels, and/or increase stability of a gene expression level.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. patent application Ser. No. 11/012,546, filed Dec. 14, 2004, now U.S. Pat. No. 7,267,965, which application is a continuation of International Patent Application No. PCT/NL03/00410, filed May 30, 2003, published in English as International Patent Publication No. WO 03/106674 on Dec. 24, 2003, which claims the benefit under 35 U.S.C. §119 of European Patent Application No. EP 02077344.6, filed Jun. 14, 2002, the entirety of each of which are hereby incorporated by reference.

STATEMENT ACCORDING TO 37 C.F.R §1.52(e)(5)—SEQUENCE LISTING SUBMITTED ON COMPACT DISC

Pursuant to 37 C.F.R. §1.52(e)(1)(iii), a compact disc containing an electronic version of the Sequence Listing has been submitted concomitant with this application, the contents of which are hereby incorporated by reference. The compact disc contains the file “P60555PC00 final.txt” which is 496 KB, and created on Dec. 14, 2004. A second compact disk is submitted and is an identical copy of the first compact disc (labeled, “copy 1” and “copy 2,” respectively).

TECHNICAL FIELD

The invention relates to the fields of medicine and cellular biology. More specifically, the invention relates to means and methods for regulating gene expression, and production of proteinaceous molecules.

BACKGROUND OF THE INVENTION

Polypeptide production at industrial scale currently provides many biologically active polypeptides for a variety of uses, including diagnostic and therapeutic pharmaceuticals, industrial catalysts and nourishment. Polypeptides are produced in a variety of host systems, including transgenic animals and plants, microbes, and cultured mammalian cells. In most cases, the host system is modified by recombinant DNA techniques, for instance resulting in introduction into the host cell of a transgene which encodes a polypeptide of interest. Such a transgene typically includes elements that influence the transcription, translation, and/or processing of the transgene's polypeptide coding sequence. A recombinant host is then identified and isolated which has a suitable yield of a polypeptide of interest, and the cell population of this recombinant host is increased to an extent that it can produce the required amount of polypeptide.

The choice of the host system depends on a number of factors including: (1) the nature and intended use of a polypeptide, and (2) the cost of production. For production of biopharmaceuticals, e.g., therapeutic proteins such as hormones, cytokines, and antibodies, the host system of choice is usually cultured mammalian cells. Considerations with respect to product use and production cost with host cells will be discussed below.

(1) For in vivo therapeutic use, a therapeutic protein must not only have the correct biological activity to alter the course of a disease. It must also do no harm. Most therapeutic proteins are exported from the cell by the secretory pathway. Secreted proteins are modified by a series of post-translational events, including glycosylation, disulfide bond formation, and proteolytic processing. The post-translational modification systems vary among different species and cell types in their detailed mechanisms of action. As a result, the same polypeptide chain can be detectably different when it is produced in different host cells. These differences can be analytical, such as differences in physical properties such as molecular mass, net electrical charge, carbohydrate composition, or structure. The differences can also be functional, affecting for instance the biological activity of the protein itself (catalytic activity, ligand binding characteristics, etc.), and/or its in vivo properties (immunogenicity, biological half life, biodistribution, etc.). Functional differences can, therefore, affect both function and possible side effect(s) of a therapeutic protein. Host cell lines that produce proteins with low efficacy are not suitable for commercial exploitation. Furthermore, host cells which produce modified protein that involves significant side effects in a patient should not be used. These factors are becoming increasingly important considerations during selection of a host cell line for production of a therapeutic protein.

(2) Therapeutic protein production in host cells is an intrinsically costly process. Current methods for industrial production of such proteins often perform poorly, resulting in products that are prohibitively expensive. Poor performance can be due to limitations of protein expression systems and host cell lines currently in use. These limitations mostly have a few specific causes, including (a) failure to identify and isolate recombinant host cell lines that have suitable productivity of proteins (poor predictability), (b) silencing, during the industrial production cycle, of the transgenes that encode proteins (poor stability), and (c) low or incorrect post-translational processing and secretory capacity of the host cell line. These limitations will be considered separately below.

(a) Conventional methods furnish only low frequencies of recombinant host cells that have suitable yields of proteins. Identifying and isolating these rare recombinant cell lines is a laborious and expensive process. The poor predictability of conventional methods means that often a recombinant host cell line is selected for production that has sub-optimal productivity characteristics, simply because a superior recombinant cell line was not identified and isolated during the selection process.

(b) Transgenes are often subject to silencing during cultivation of recombinant host cells. Silencing acts by suppressing transcription of a transgene. Detailed mechanisms of silencing are still not known, and different conventional methods are prone to different kinds of silencing phenomena. With one phenomenon, an individual transgene is silenced by formation of transcriptionally refractory heterochromatin at the transgenic locus. Heterochromatin formation is influenced by the position of genomic integration of a transgene (“position effects” (Boivin and Dura, 1998)). Transgene integration occurs more or less at random. Since most of the genome is heterochromatin, most transgene loci are prone to silencing due to position effects.

A second transgene-silencing phenomenon can occur when two or more copies of a transgene are integrated into a genome during construction of a recombinant cell line. Formation of tandem transgene repeats often occurs during the initial integration step. Furthermore, in order to increase product yield, many recombinant host cell lines are engineered after the integration step to amplify the copy number of a transgene, which also results in tandem transgene repeats (Kaufman, 1990). Tandem repeats and other configurations of multiple transgene copies are particularly prone to silencing (“repeat-induced gene silencing” (Garrick et al., 1998)).

In case that a genome contains multiple copies of a transgene, the yield can also decline via another phenomenon than transcriptional silencing. The number of copies of the transgene can decline during cultivation of a recombinant host cell line. The productivity of such cell lines at the time of selection for use is correlated with a transgene copy number, and consequently as copies of a transgene are lost, the yield declines (Kaufman, 1990).

(c) Different cell types in a mammalian organism have different capacities for post-translational modification and secretion of proteins. The functions of some cell types include production of large quantities of secreted proteins; examples include lymphocytes (producing immunoglobulins), hepatocytes (producing serum proteins), and fibroblasts (producing extracellular matrix proteins). These cell types are favorable sources for deriving host cell lines for production of secreted heterologous proteins. More favorable is the use of a cell line whose progenitor organismal cell type secretes a protein or class of proteins of interest. For example, it is particularly favorable to express recombinant monoclonal antibodies in lymphocytes (or host cells derived from lymphocytes), erythropoietin in hepatocytes (or host cells derived from hepatocytes), and blood clotting factors (e.g., Factor VIII and van Willebrand's factor) in endothelial cells (or host cells derived from endothelial cells).

The use of specific cell types (or cell lines derived therefrom) for production of their affiliated proteins is favorable because such specific cell types will carry out proper post-translational modifications of produced proteins. However, specific cell types often do not have high secretory capacities. For example, cells of the central nervous system, such as neurons, have low intrinsic protein secretion capacities. These cells do secrete proteins, however, including neurotrophins. Neurotrophins regulate the fate and shape of neuronal cells during fetal and juvenile development. Moreover, they influence patterns of neuronal degeneration and regeneration in adults (Bibel and Barde, 2000). Production of neurotrophins for therapeutic applications has considerable biopharmaceutical value (e.g., Axokine™, recombinant ciliary neurotrophic factor from Regeneron). In order to produce heterologous neurotrophins with post-translational modifications (and hence functional properties) that match the naturally-occurring proteins, expression in host cells derived from the central nervous system is favorable. However, production of polypeptides such as neurotrophins in host cell lines such as those derived from neural tissue is inefficient using conventional methods. The predictability of identifying high-expressor isolates from these types of cell lines is often poor; the yield of proteins from such cell lines is generally low, and production levels are characteristically unstable.

Another drawback to a use of specific host cells for production of affiliated proteins is that it is usually difficult to isolate cell lines with favorable biotechnological characteristics. These characteristics for instance include the mode and rate of growth, and the ease of introduction of a transgene. Consequently, various general host cell lines have been established. Examples of these include CHO cells from Chinese hamster ovary (ATCC (American Type Culture Collection) CCL-61), BHK cells from baby hamster kidney (ATCC CCL-10), and Vero cells from African green monkey kidney (ATCC CCL-81). These “general purpose” host cell lines are widely used for production of a number of heterologous proteins. A disadvantage of general purpose cell lines is that the post-translational modifications of heterologous proteins produced by them often differ from the post-translational modifications of the naturally occurring proteins. These differences can have functional consequences resulting in side effects, as discussed above.

Table 1 lists a number of proteins that are currently in use or under development for biopharmaceutical applications. It also lists the tissue or cell type in which each protein is normally produced in the human body. These 24 proteins (or protein classes) come from a wide range of cells and tissue, ranging from highly secretory cells (hepatocytes, endothelial cells) to cells with low secretory capacity (e.g., neural tissue). Currently, neither general-purpose host cells nor specific host cells have qualities that enable optimal expression of the broad spectrum of biopharmaceutically important secreted proteins.

Hence, protein production by conventional host cell lines involves a lot of disadvantages and complications, for instance with respect to yield and post-translational modifications. There is a need in the art for improved protein production in recombinant host cell lines.

SUMMARY OF THE INVENTION

The present invention provides a method for producing a proteinaceous molecule in a cell comprising selecting a cell for its suitability for producing the proteinaceous molecule, providing a nucleic acid encoding the proteinaceous molecule with a nucleic acid comprising a STAR (STabilizing Anti-Repression) sequence, expressing the resulting nucleic acid in the cell and collecting the proteinaceous molecule.

The STAR sequence has to be operably linked to the nucleic acid encoding the proteinaceous molecule in order to be effective. In one embodiment of the invention, one STAR element is used. Preferably however, more than one STAR element is used. In a particularly preferred embodiment, the nucleic acid encoding the proteinaceous molecule is provided with two STAR sequences; one STAR sequence at the 5′ side of the coding sequence of the nucleic acid and one STAR sequence at the 3′ side of the coding sequence of the nucleic acid.

Description of STAR Elements

New transcription regulatory elements were disclosed by the present inventors, which are named STAR sequences (See EP 01202581.3). STAR sequences are nucleic acid sequences that comprise a capacity to influence transcription of genes in cis. Typically, although not necessarily, the STAR sequences do not code by themselves for a functional protein.

A STAR sequence has a gene transcription modulating quality in at least one type of cell. A STAR sequence is capable of enhancing gene transcription resulting in a higher yield, increasing the proportion of transgene-comprising host cells with acceptable expression levels, and/or increasing stability of transgenes in recombinant cell lines.

In EP 01202581.3 a method of detecting, and optionally selecting, a STAR sequence is provided, comprising providing a transcription system with a variety of a fragment-comprising vectors, the vectors comprising i) an element with a gene-transcription repressing quality, and ii) a promoter directing transcription of a reporter gene, the method further comprising performing a selection step in the transcription system in order to identify the STAR sequence. In a preferred embodiment, the fragments are located between i) the element with a gene-transcription repressing quality, and ii) the promoter directing transcription of the reporter gene. RNA polymerase initiates the transcription process after binding to a specific sequence, called the promoter, that signals where RNA synthesis should begin. A STAR sequence can enhance transcription from the promoter in cis, in a given cell type and/or a given promoter.

Methods disclosed in EP 01202581.3 have been used to isolate STAR elements from the human genome. Isolated human STAR elements have been placed in DNA vectors so as to flank transgene expression units, and the vectors have subsequently been integrated into host cell genomes. Transgene expression in these recombinant host cells has been compared to expression in similar host cells in which the expression units are not flanked by STAR elements. The results show that STAR elements have at least one of three consequences for production of (heterologous) proteinaceous molecule (also referred to as (heterologous) protein): (1) they increase the predictability of identifying host cell lines that express a proteinaceous molecule at industrially acceptable levels; (2) they result in host cell lines with increased protein yields; and/or (3) they result in host cell lines that exhibit more stable protein production during prolonged cultivation. Each of these attributes is discussed in more detail below:

(1) Increased predictability: Integration of transgene expression units can occur at random positions throughout the host cell genome. However, much of the genome is transcriptionally silent heterochromatin. When the expression units include STAR elements flanking the transgene, the position of integration has a reduced effect on expression. The STAR elements impair the ability of adjacent heterochromatin to silence the transgene. Consequently, the proportion of transgene-containing host cells with acceptable expression levels is increased.

(2) Yield: The levels of protein expression in primary populations of recombinant host cells, directly after transgene integration, have been surveyed. The expression level of individuals in the populations varies. However, when the transgenes are protected by STAR elements, the variability is reduced. This reduced variability is most conspicuous in that fewer clones are recovered that have low levels of expression. Furthermore, the populations with STAR elements commonly have individuals with strikingly high expression. These high-yielding individuals are favorable for production of proteinaceous molecules.

(3) Increased stability: STAR elements increase the stability of transgenes in recombinant host cell lines by ensuring that the transgenes are not transcriptionally silenced during prolonged cultivation. Comparative trials show that, under conditions in which transgenes that are not protected by STAR elements are progressively silenced (5 to 25 passages in cultivation), STAR element-protected transgenes continue to be expressed at high levels. This is an advantage during industrial production of proteinaceous molecules, during which cell cultivation continues for prolonged periods, from a few weeks to many months.

Hence, a STAR sequence can enhance expression of a heterologous proteinaceous molecule. In addition, a STAR sequence can enhance expression of a naturally produced proteinaceous molecule.

Transcription can be influenced through a direct effect of the STAR sequence (or the protein(s) binding to it) on the transcription of a particular promoter. Transcription can however, also be influenced by an indirect effect, for instance because the STAR sequence affects the function of one or more other regulatory elements. A STAR sequence can also comprise a stable gene transcription quality. Frequently, expression levels drop dramatically with increasing numbers of cell divisions. With the methods disclosed in EP 01202581.3 it is possible to detect and optionally select a DNA sequence that is capable of at least in part preventing the dramatic drop in transcription levels with increasing numbers of cell divisions. Strikingly, fragments comprising a STAR sequence can be detected and optionally selected with a method EP 01202581.3, in spite of the fact that the method does not necessarily measure long term stability of transcription.

A STAR sequence is suitable for enhancing the level of transcription of a gene of interest in a host cell. If, together with a gene of interest, a STAR sequence is also introduced into host cells, more clones can be detected that express more than a certain amount of the gene of interest. As used herein, such host cells are termed “host cells with acceptable expression levels.”

Furthermore, if, together with a gene of interest, a STAR sequence is also introduced into host cells, a higher yield of produced proteinaceous molecules can be obtained, while gene expression level is also more stable than in the absence of such STAR sequences. Preferably, a STAR sequence derived from a plant and/or vertebrate is used. More preferably a human STAR sequence is used.

Sequences comprising a STAR sequence can be found by using a functional assay, as described above. However, once a collection of such sequences has been identified, bioinformatics can be used to find other STAR sequences. Several methods are available in the art to extract sequence identifiers from a family of DNA sequences sharing a certain common feature. Such sequence identifiers can subsequently be used to identify sequences that share one or more identifiers. Sequences sharing such one or more identifiers are likely to be a member of the same family of sequences, i.e., are likely to share the common feature of the family. By the present inventors a large number of sequences comprising STAR activity (so-called STAR sequences) were used to obtain sequence identifiers (patterns) which are characteristic for sequences comprising STAR activity. These patterns can be used to determine whether a test sequence is likely to contain STAR activity. A method for detecting the presence of a STAR sequence within a nucleic acid sequence of about 50-5000 base pairs is thus provided, comprising determining the frequency of occurrence in the sequence of at least one sequence pattern and determining that the frequency of occurrence is representative of the frequency of occurrence of at least one sequence pattern in at least one sequence comprising a STAR sequence. In principle any method is suited for determining whether a sequence pattern is representative of a STAR sequence. Many different methods are available in the art. Preferably, the step of determining that the occurrence is representative of the frequency of occurrence of at least one sequence pattern in at least one sequence comprising a STAR sequence comprises, determining that the frequency of occurrence of at least one sequence pattern significantly differs between at least one STAR sequence and at least one control sequence. In principle any significant difference is discriminative for the presence of a STAR sequence. However, in a particularly preferred embodiment, the frequency of occurrence of at least one sequence pattern is significantly higher in at least one sequence comprising a STAR sequence compared to at least one control sequence.

A considerable number of sequences comprising a STAR sequence have been identified by the present inventors. It is possible to use these sequences to test how efficient a pattern is in discriminating between a control sequence and a sequence comprising a STAR sequence. Using so-called discriminant analysis it is possible to determine on the basis of any set of STAR sequences in a species, the most optimal discriminative sequence patterns or combination thereof. Thus, preferably, at least one of the patterns is selected on the basis of optimal discrimination between at least one sequence comprising a STAR sequence and a control sequence.

In a preferred embodiment, the frequency of occurrence of a sequence pattern in a test nucleic acid is compared with the frequency of occurrence in a sequence known to contain a STAR sequence. In this case, a pattern is considered representative for a sequence comprising a STAR sequence if the frequencies of occurrence are similar. In a preferred embodiment, another criterion is used. The frequency of occurrence of a pattern in a sequence comprising a STAR sequence is compared to the frequency of occurrence of the pattern in a control sequence. By comparing the two frequencies it is possible to determine for each pattern thus analyzed, whether the frequency in the sequence comprising the STAR sequence is significantly different from the frequency in the control sequence. In this embodiment, a sequence pattern is considered to be representative of a sequence comprising a STAR sequence, if the frequency of occurrence of the pattern in at least one sequence comprising a STAR sequence is significantly different from the frequency of occurrence of the same pattern in a control sequence. By using larger numbers of sequences comprising a STAR sequence the number of patterns for which a statistical difference can be established increases, thus enlarging the number of patterns for which the frequency of occurrence is representative for a sequence comprising a STAR sequence. Preferably, the frequency of occurrence is representative of the frequency of occurrence of at least one sequence pattern in at least two sequences comprising a STAR sequence; more preferably, in at least five sequences comprising a STAR sequence; and, even more preferably, in at least ten sequences comprising a STAR sequence. More preferably, the frequency of occurrence is representative of the frequency of occurrence of at least one sequence pattern in at least 20 sequences comprising a STAR sequence. In a particularly preferred embodiment, the frequency of occurrence is representative of the frequency of occurrence of at least one sequence pattern in at least 50 sequences comprising a STAR.

The patterns that are indicative for a sequence comprising a STAR sequence are also dependent on the type of control nucleic acid used. The type of control sequence used is preferably selected on the basis of the sequence in which the presence of a STAR sequence is to be detected. In a preferred embodiment, the control sequence comprises a random sequence comprising a similar AT/CG content as at least one sequence comprising a STAR sequence. In another preferred embodiment, the control sequence is derived from the same species as the sequence comprising the STAR sequence. For instance, if a test sequence is scrutinized for the presence of a STAR sequence, active in a plant cell, then preferably the control sequence is also derived from a plant cell. Similarly, for testing for STAR activity in a human cell, the control nucleic acid is preferably also derived from a human genome. In a preferred embodiment, the control sequence comprises between 50% and 150% of the bases of at least one sequence comprising a STAR sequence. In a particularly preferred embodiment, the control sequence comprises between 90% and 110% of the bases of at least one sequence comprising a STAR sequence. More preferably, between 95% and 105%.

A pattern can comprise any number of bases larger than two. Preferably, at least one sequence pattern comprises at least five, more preferably at least six, bases. In another embodiment, at least one sequence pattern comprises at least eight bases. In a preferred embodiment, the at least one sequence pattern comprises a pattern listed in Table 6 and/or Table 7. A pattern may consist of a consecutive list of bases. However, the pattern may also comprise bases that are interrupted one or more times by a number of bases that are not or only partly discriminative. A partly discriminative base is, for instance, indicated as a purine.

Preferably, the presence of STAR activity is verified using a functional assay. Several methods are presented herein to determine whether a sequence comprises STAR activity. STAR activity is confirmed if the sequence is capable of performing at least one of the following functions: (i) at least in part inhibiting the effect of sequence comprising a gene transcription repressing element of the invention, (ii) at least in part blocking chromatin-associated repression, (iii) at least in part blocking activity of an enhancer, (iv) conferring upon an operably linked nucleic acid encoding a transcription unit compared to the same nucleic acid alone, (iv-a) a higher predictability of transcription, (iv-b) a higher transcription, and/or (iv-c) a higher stability of transcription over time.

The large number of sequences comprising STAR activity identified by the present inventors open up a wide variety of possibilities to generate and identify sequences comprising the same activity in kind not necessarily in amount. For instance, it is well within the reach of a skilled person to alter the sequences identified in the present invention and test the altered sequence for STAR activity. Such altered sequences are, therefore, also part of the present invention. Alteration can include deletion, insertion and mutation of one or more bases in the sequences.

Sequences comprising STAR activity were identified in stretches of 400 bases. However, it is expected that not all of these 400 bases are required to retain STAR activity. Methods to delimit the sequences that confer a certain property to a fragment of between 400 and 5000 bases are well known. The minimal sequence length of a fragment comprising STAR activity is estimated to be about 50 bases.

Table 6 (SEQ ID NOS:177-342) and Table 7 (SEQ ID NOS:343-1072) list patterns of six bases that have been found to be over represented in nucleic acid molecules comprising STAR activity. This over representation is considered to be representative for a STAR sequence. The tables were generated for a family of 65 STAR sequences (SEQ ID NOS:1-65). Similar tables can be generated starting from a different set of STAR sequences, or from a smaller or larger set of STAR sequences. A pattern is representative for a STAR sequence if it is over represented in the STAR sequence compared to a sequence not comprising a STAR element. This can be a random sequence. However, to exclude a non relevant bias, the sequence comprising a STAR sequence is preferably compared to a genome or a significant part thereof. Preferably, a genome of a vertebrate or plant, more preferably, a human genome. A significant part of a genome is, for instance, a chromosome. Preferably the sequence comprising a STAR sequence and the control sequence are derived from nucleic acid of the same species.

The more STAR sequences are used for the determination of the frequency of occurrence of sequence patterns, the more representative for STARs the patterns are that are over- or under-represented. Considering that many of the functional features that can be expressed by nucleic acids are mediated by proteinaceous molecules binding to them, it is preferred that the representative pattern is over-represented in the STAR sequences. Such over-represented pattern can be part of a binding site for such a proteinaceous molecule. Preferably, the frequency of occurrence is representative of the frequency of occurrence of at least one sequence pattern in at least two sequences comprising a STAR sequence; more preferably, in at least five sequences comprising a STAR sequence; and, even more preferably, in at least ten sequences comprising a STAR sequence. More preferably, the frequency of occurrence is representative of the frequency of occurrence of at least one sequence pattern in at least 20 sequences comprising a STAR sequence. In a particularly preferred embodiment, the frequency of occurrence is representative of the frequency of occurrence of at least one sequence pattern in at least 50 sequences comprising a STAR. Preferably, the sequences comprising a STAR sequence comprises at least one of the sequences depicted in the sequences comprising STAR1-STAR65 (SEQ ID NOS:1-65), sequences comprising STAR66 and testing set (SEQ ID NOS:66-84), and sequences comprising Arabidopsis STAR A1-A35 (SEQ ID NOS:85-119) (hereinafter SEQ ID NOS:1-119).

STAR activity is a feature shared by the sequences listed in SEQ ID NOS:1-119. However, this does not mean that they must all share the same identifier sequence. It is very well possible that different identifiers exist. Identifiers may confer this common feature onto a fragment containing it, though this is not necessarily so.

By using more sequences comprising STAR activity for determining the frequency of occurrence of a sequence pattern or patterns, it is possible to select patterns that are more often than others present or absent in such a STAR sequence. In this way it is possible to find patterns that are very frequently over- or under-represented in STAR sequences. Frequently, over- or under-represented patterns are more likely to identify candidate STAR sequences in test sets. Another way of using a set of over- or under-represented patterns is to determine which pattern or combination of patterns is best suited to identify a STAR in a sequence. Using so-called discriminative statistics, we have identified a set of patterns that performs best in identifying a sequence comprising a STAR element. In a preferred embodiment, at least one of the sequence patterns for detecting a STAR sequence comprises a sequence pattern GGACCC (SEQ ID NO:464), CCCTGC (SEQ ID NO:816), AAGCCC (SEQ ID NO:270), CCCCCA (SEQ ID NO:298) and/or AGCACC (SEQ ID NO:336). In another embodiment, at least one of the sequence patterns for detecting a STAR sequence comprises a sequence pattern CCCN{16}AGC (SEQ ID NO:415), GGCN{9}GAC (SEQ ID NO:536), CACN{13}AGG (SEQ ID NO:761), and/or CTGN{4}GCC (SEQ ID NO:839).

A list of STAR sequences can also be used to determine one or more consensus sequences therein. The invention, therefore, also provides a consensus sequence for a STAR element. This consensus sequence can of course be used to identify candidate STAR elements in a test sequence.

Moreover, once a sequence comprising a STAR element has been identified in a vertebrate it can be used by means of sequence homology to identify sequences comprising a STAR element in other species belonging to vertebrate. Preferably a mammalian STAR sequence is used to screen for STAR sequences in other mammalian species. Similarly, once a STAR sequence has been identified in a plant species, it can be used to screen for homologous sequences with similar function in other plant species. The invention in one aspect provides a STAR sequence obtainable by a method according to the invention. Further provided is a collection of STAR sequences. Preferably, the STAR sequence is a vertebrate or plant STAR sequence. More preferably, the STAR sequence is a mammalian STAR sequence or an angiosperm (monocot, such as rice or dicot, such as Arabidopsis). More preferably, the STAR sequence is a primate and/or human STAR sequence.

A list of sequences comprising STAR activity can be used to determine whether a test sequence comprises a STAR element. There are, as mentioned above, many different methods for using such a list for this purpose. In a preferred embodiment, the invention provides a method for determining whether a nucleic acid sequence of about 50-5000 base pairs comprises a STAR sequence, the method comprising: generating a first table of sequence patterns comprising the frequency of occurrence of the patterns in a collection of STAR sequences of the invention; generating a second table of the patterns comprising the frequency of occurrence of the patterns in at least one reference sequence; selecting at least one pattern of which the frequency of occurrence differs between the two tables; determining, within the nucleic acid sequence of about 50-5000 base pairs, the frequency of occurrence of at least one of the selected patterns; and determining whether the occurrence in the test nucleic acid is representative of the occurrence of the selected pattern in the collection of STAR sequences. Alternatively, determining comprises determining whether the frequency of occurrence in the test nucleic acid is representative of the frequency occurrence of the selected pattern in the collection of STAR sequences. Preferably, the method further comprises determining whether the candidate STAR comprises a gene transcription modulating quality using a method of the invention. Preferably, the collection of STARS comprises sequence as depicted in SEQ ID NOS:1-119. In another aspect, the invention provides an isolated and/or recombinant nucleic acid sequence comprising a STAR sequence obtainable by a method of the invention.

As mentioned above, a STAR sequence can exert its activity in a directional way, i.e., more to one side of the fragment containing it than to the other. Moreover, STAR activity can be amplified in amount by multiplying the number of STAR elements. The latter suggests that a STAR element may comprise one or more elements comprising STAR activity. Another way of identifying a sequence capable of conferring STAR activity on a fragment containing it comprises selecting from a vertebrate or plant sequence, a sequence comprising STAR activity and identifying whether the selected sequence and sequences flanking the selected sequence are conserved in another species. Such conserved flanking sequences are likely to be functional sequences. In one aspect, the invention, therefore, provides a method for identifying a sequence comprising a STAR element comprising selecting a sequence of about 50 to 5000 base pairs from a vertebrate or plant species comprising a STAR element and identifying whether sequences flanking the selected sequence in the species are conserved in at least one other species. The invention, therefore, further provides a method for detecting the presence of a STAR sequence within a nucleic acid sequence of about 50-5000 base pairs, comprising identifying a sequence comprising a STAR sequence in a part of a chromosome of a cell of a species and detecting significant homology between the sequence and a sequence of a chromosome of a different species. Preferably, the species comprises a plant or vertebrate species, ideally a mammalian species. The invention also provides a method for detecting the presence of a STAR element within a nucleic acid sequence of about 50-5000 base pairs of a vertebrate or plant species, comprising identifying whether a flanking sequence of the nucleic acid sequence is conserved in at least one other species.

It is important to note that methods of the invention for detecting the presence of a sequence comprising a STAR sequence using bioinformatical information are iterative in nature. The more sequences comprising a STAR sequence are identified with a method of the invention, the more patterns are found to be discriminative between a sequence comprising a STAR sequence and a control sequence. Using these newly found discriminative patterns, more sequences comprising a STAR sequence can be identified, which, in turn, enlarges the set of patterns that can discriminate and so on. This iterative aspect is an important aspect of methods provided in the present invention.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a diagram illustrating the pSelect plasmid used for isolating STAR elements. The zeocin resistance gene is under control of the SV40 promoter, and is upstream of the SV40 polyadenylation site. Upstream of the SV40 promoter is a tandem array of lexA operator sites. Between the lexA operators and the SV40 promoter is a cloning site; test DNAs (e.g., size-fractionated genomic DNA) are cloned into the BamHI site. The plasmid also has the hygromycin resistance gene (hygro) for selection of transformed cells, the EBNA-1 and oriP sequences for plasmid replication in mammalian cells, and the ampicillin resistance gene (ampR) and ori sequence for propagation in Escherichia coli.

FIG. 2 is a diagram depicting the pSDH-CSP plasmid used for testing STAR activity. The Secreted Alkaline Phosphatase (SEAP) reporter gene is under control of the CMV promoter, and the puromycin resistance selectable marker (puro) is under control of the SV40 promoter. Flanking these two genes are multiple cloning sites (MCSI and MCSII) into which STAR elements can be cloned. The plasmid also has an origin of replication (ori) and ampicillin resistance gene (amp^R) for propagation in Escherichia coli.

FIG. 3 is a graph showing that STAR6 (SEQ ID NO:6) and STAR8 (SEQ ID NO:8) improve predictability and yield of transgene expression in U-2 OS cells. Expression of luciferase from the CMV promoter by U-2 OS cells transfected with pSDH-CMV, pSDH-CMV-STAR6, or pSDH-CMV-STAR8 was determined. The STAR-containing constructs confer greater predictability and elevated yield relative to the pSDH-CMV construct alone.

FIG. 4 is a graph illustrating that STAR6 (SEQ ID NO:6), but not STAR8 (SEQ ID NO:8), improves predictability and yield of transgene expression in CHO cells. Expression of SEAP from the CMV promoter by CHO cells transfected with pSDH-CSP, pSDH-CSP-STAR6, or pSDH-CSP-STAR8 was determined. The STAR6-containing constructs confer greater predictability and elevated yield relative to the pSDH-CSP construct alone, identifying STAR6 (SEQ ID NO:6) as a promiscuous STAR element. In contrast, the STAR8-containing constructs do not consistently increase yield or predictability relative to the pSDH-CSP construct, suggesting that STAR8 (SEQ ID NO:8) is a cell line-specific STAR element.

FIG. 5 is a graph depicting that STAR6 (SEQ ID NO:6) and STAR49 (SEQ ID NO:49) improve predictability and yield of transgene expression. Expression of SEAP from the CMV promoter by CHO cells transfected with pSDH-CSP, pSDH-CSP-STAR6, or pSDH-CSP-STAR49 was determined. The STAR-containing constructs confer greater predictability and elevated yield relative to the pSDH-CSP construct alone.

FIG. 6 is a graph showing the minimal essential sequences of STAR10 (SEQ ID NO:10) and STAR27 (SEQ ID NO:27). Portions of the STAR elements were amplified by PCR: STAR10 (SEQ ID NO:10) was amplified with primers E23 (SEQ ID NO:166) and E12 (SEQ ID NO:155) to yield fragment 10A (corresponding approximately to the first 400 nucleotides of SEQ ID NO:10), E13 (SEQ ID NO:156) and E14 (SEQ ID NO:157) to yield fragment 10B (corresponding approximately to the second 400 nucleotides of SEQ ID NO:10), and E15 (SEQ ID NO:158) and E16 (SEQ ID NO:159) to yield fragment 10C (corresponding approximately to the third 400 nucleotides of SEQ ID NO:10). STAR27 (SEQ ID NO:27) was amplified with primers E17 (SEQ ID NO:160) and E18 (SEQ ID NO:161) to yield fragment 27A (corresponding approximately to the first 500 nucleotides of SEQ ID NO:27), E19 (SEQ ID NO:162) and E20 (SEQ ID NO:163) to yield fragment 27B (corresponding to the second 500 nucleotides of SEQ ID NO:27), and E21 (SEQ ID NO:164) and E22 (SEQ ID NO:165) to yield fragment 27C (corresponding approximately to the third 500 nucleotides of SEQ ID NO:27). These sub-fragments were cloned into the pSelect vector. After transfection into U-2 OS/Tet-Off/LexA-HP1 cells, the growth of the cultures in the presence of zeocin was monitored. Growth rates varied from vigorous (+++) to poor (+/−), while some cultures failed to survive zeocin treatment (−) due to absence of STAR activity in the DNA fragment tested.

FIG. 7 is a graph illustrating the STAR element function in the context of the SV40 promoter. pSDH-SV40 and pSDH-SV40-STAR6 were transfected into the human osteosarcoma U-2 OS cell line, and expression of luciferase was assayed with or without protection from gene silencing by STAR6 (SEQ ID NO:6) in puromycin-resistant clones.

FIG. 8 is a graph showing the STAR element function in the context of the Tet-Off promoter. pSDH-Tet and pSDH-Tet-STAR6 were transfected into the human osteosarcoma U-2 OS cell line, and expression of luciferase was assayed with or without protection from gene silencing by STAR6 (SEQ ID NO:6) in puromycin-resistant clones.

FIG. 9 is a schematic diagram of the orientation of STAR elements as they are cloned in the pSelect vector (panel A), as they are cloned into pSDH vectors to preserve their native orientation (panel B), and as they are cloned into pSDH vector in the opposite orientation (panel C).

FIG. 10 is a graph showing directionality of STAR66 (SEQ ID NO:66) function. The STAR66 (SEQ ID NO:66) element was cloned into pSDH-Tet in either the native (STAR66 native) or the opposite orientation (STAR66 opposite) and transfected into U-2 OS cells. Luciferase activity was assayed in puromycin resistant clones.

FIG. 11 is a southern blot showing copy number-dependence of STAR function. Southern blot of luciferase expression units in pSDH-Tet-STAR10, integrated into U-2 OS genomic DNA. Radioactive luciferase DNA probe was used to detect the amount of transgene DNA in the genome of each clone, which was then quantified with a phosphorimager.

FIG. 12 is a graph illustrating copy number-dependence of STAR function. The copy number of pSDH-Tet-STAR10 expression units in each clone was determined by phosphorimagery and compared with the activity of the luciferase reporter enzyme expressed by each clone.

FIG. 13 is a schematic diagram and graphs depicting enhancer-blocking and enhancer assays. The luciferase expression vectors used for testing STARs for enhancer-blocking and enhancer activity are shown schematically. The E-box binding site for the E47 enhancer protein is upstream of a cloning site for STAR elements. Downstream of the STAR cloning site is the luciferase gene under control of a human alkaline phosphatase minimal promoter (mp). The histograms indicate the expected outcomes for the three possible experimental situations (see text). Panel A: Enhancer-blocking assay. Panel B: Enhancer assay.

FIG. 14 is a graph showing enhancer-blocking assay. Luciferase expression from a minimal promoter is activated by the E47/E-box enhancer in the empty vector (vector). Insertion of enhancer-blockers (scs, HS4) or STAR elements (

STAR elements

1, 2, 3, 6, 10, 11, 18, and 27; SEQ ID NOS:1, 2, 3, 6, 10, 11, 18 and 27, respectively) block luciferase activation by the E47/E-box enhancer.

FIG. 15 is a graph illustrating enhancer assay. Luciferase expression from a minimal promoter is activated by the E47/E-box enhancer in the empty vector (E47). Insertion of the scs and HS4 elements or various STAR elements (

STARs

1, 2, 3, 6, 10, 11, 18, and 27; SEQ ID NOS:1, 2, 3, 6, 10, 11, 18 and 27, respectively) do not activate transcription of the reporter gene.

FIG. 16 illustrates STAR18 (SEQ ID NO:18) sequence conservation between mouse and human. The region of the human genome containing 497 base pair STAR18 (SEQ ID NO:18) is shown (black boxes); the element occurs between the HOXD8 and HOXD4 homeobox genes on human chromosome 2. It is aligned with a region in mouse chromosome 2 that shares 72% sequence identity. The region of human chromosome 2 immediately to the left of STAR18 (SEQ ID NO:18) is also highly conserved with mouse chromosome 2 (73% identity; gray boxes); beyond these region, the identity drops below 60%. The ability of these regions from human and mouse, either separately or in combination, to confer growth on zeocin is indicated: −, no growth; +, moderate growth; ++, vigorous growth; +++, rapid growth.

FIG. 17 is a schematic diagram of bio-informatic analysis workflow. For details, see text.

FIG. 18 is a schematic diagram showing the results of discriminant analysis on classification of the training set of 65 STAR elements. STAR elements that are correctly classified as STARs by Stepwise Linear Discriminant Analysis (LDA) are shown in a Venn diagram. The variables for LDA were selected from frequency analysis results for hexameric oligonucleotides (“oligos”) and for dyads. The diagram indicates the concordance of the two sets of variables in correctly classifying STARs.

FIG. 19 is a graph illustrating that U-2 OS/Tet-Off/lexA-HP1 cells were transfected with candidate Arabidopsis STAR elements and cultivated at low doxycycline concentrations. Total RNA was isolated and subjected to RT-PCR; the bands corresponding to the zeocin and hygromycin resistance mRNAs were detected by Southern blotting and quantified with a phosphorimager. The ratio of the zeocin to hygromycin signals is shown for transfectants containing zeocin expression units flanked by 12 different Arabidopsis STAR elements, the Drosophila scs element, or no flanking element.

FIG. 20 is a schematic diagram and graph illustrating that STAR elements improve GFP expression in CHO cells. The ppGIZ and ppGIZ-STAR7 plasmids used for testing STAR activity are shown. The expression unit comprises (from 5′ to 3′) a transgene (encoding for the GFP protein), an IRES, and a selectable marker (zeo, conferring zeocin resistance) under control of the CMV promoter. The expression unit has the SV40 transcriptional terminator at its 3′ end (t). The entire cassette with the expression unit is either flanked by STAR7 (SEQ ID NO:7) elements (STAR7-shielded) or not (Control). The constructs are transfected to CHO-K1 cells. Stable colonies are expanded and the GFP signal is determined on a XL-MCL Beckman Coulter flow cytometer. For each independent colony the mean of the GFP signal is plotted. This is taken as measure for the level of GFP expression. The results in FIG. 20 show that in CHO cells the STAR7-shielded construct confers greater predictability and elevated GFP expression relative to the ppGIZ control construct alone.

FIG. 21 is a schematic diagram and graph showing that STAR elements improve GFP expression in NSO cells. The ppGIZ and ppGIZ-STAR7 plasmids used for testing STAR activity are shown as in FIG. 20. The constructs are transfected to NSO cells. Stable colonies are expanded and the GFP signal is determined on a XL-MCL Beckman Coulter flow cytometer. For each independent colony the mean of the GFP signal is plotted. This is taken as measure for the level of GFP expression. The results in FIG. 21 show that in NSO cells the STAR7-shielded (SEQ ID NO:7) construct confers greater predictability and elevated GFP expression relative to the ppGIZ control construct alone.

FIG. 22 is a schematic diagram and graph depicting that STAR elements improve GFP expression in 293 cells. The ppGIZ and ppGIZ-STAR7 plasmids used for testing STAR activity are shown as in FIG. 20. The constructs are transfected to 293 cells. Stable colonies are expanded and the GFP signal is determined on a XL-MCL Beckman Coulter flow cytometer. For each independent colony, the mean of the GFP signal is plotted. This is taken as measure for the level of GFP expression. The results in FIG. 22 show that in 293 cells the STAR7-shielded (SEQ ID NO:7) construct confers greater predictability and elevated GFP expression relative to the ppGIZ control construct alone.

DETAILED DESCRIPTION OF THE INVENTION Definitions

Quality

The term “quality” in relation to a sequence refers to an activity of the sequence.

STAR and STAR Sequence

The terms “STAR,” “STAR sequence” or “STAR element,” as used herein, refer to a DNA sequence comprising one or more of the mentioned gene transcription modulating qualities.

DNA Sequence

The term “DNA sequence” as used herein, unless otherwise specified, does not refer to a listing of specific ordering of bases, but rather to a physical piece of DNA. A transcription quality with reference to a DNA sequence refers to an effect that the DNA sequence has on transcription of a gene of interest. “Quality” as used herein refers to detectable properties or attributes of a nucleic acid or protein in a transcription system.

Proteinaceous Molecule

By a “proteinaceous molecule” is meant herein a molecule comprising amino acids. At least a part of the amino acids are bound to each other to form a peptide. Preferably, the proteinaceous molecule comprises a polypeptide. In this application, the term “proteinaceous molecule” also includes “polypeptide.”

Essentially the Same Properties

By “essentially the same properties” is meant that the properties are essentially the same in kind, not necessarily in amount. For instance, if a proteinaceous molecule has essentially the same properties as a pharmaceutically active compound, the proteinaceous molecule also displays such pharmaceutical activity in kind, not necessarily in amount.

Naturally Occurring Proteinaceous Molecule of the Same Kind

By a “naturally occurring proteinaceous molecule of the same kind” is meant a proteinaceous molecule with the same primary structure, which is naturally produced in vivo, not influenced by human interference. Examples comprise an antibody produced in vivo by a lymphocyte and erythropoietin produced in vivo by a hepatocyte.

Host Cell, Host Cell Line

As used herein, the terms “host cell” and “host cell line” refer to a cell and to homogeneous populations thereof that are capable of expressing a nucleic acid encoding a proteinaceous molecule.

Recombinant Host Cell, Recombinant Host Cell Line

The terms “recombinant host cell” and “recombinant host cell line” refer to a host cell and to homogeneous populations thereof into which a nucleic acid has been introduced.

Expression

As used herein, the term “expression” refers to production of a proteinaceous molecule, encoded by a nucleic acid. The production, for instance, involves transcription of a DNA sequence, translation of the corresponding mRNA sequence, and/or posttranslational modification. In case of secreted proteins, it can also refer to the processes of transcription, translation, and/or post-translational modification (e.g., glycosylation, disulfide bond formation, etc.), followed by exocytosis. In the case of multimeric proteins, it can include assembly of the multimeric structure from the polypeptide monomers.

Silencing

The term “silencing” refers to diminution of a level of expression of a gene or genes, including transgenes, typically over time. The expression level can be diminished but still detectable, or diminished below the threshold of detection.

Enhanced Expression

As used herein, “enhanced expression” of a gene encoding a proteinaceous molecule, or enhanced production of a proteinaceous molecule, can either involve a higher yield of the proteinaceous molecule, a higher proportion of host cells with acceptable expression levels, and/or a higher stability of a gene expression level.

Affiliated Proteinaceous Molecule of a Cell

By an “affiliated proteinaceous molecule of a cell” is meant a proteinaceous molecule which is naturally produced by the kind of cell in the organism from which the cell is derived.

For instance, erythropoietin is an affiliated proteinaceous molecule of a hepatocyte, or of a hepatocyte-derived cell line. Likewise, an antibody is an affiliated proteinaceous molecule of a lymphocyte, or of a lymphocyte-derived cell line, typically of a B-cell or a B-cell derived cell line.

Specific Host Cell Line

A “specific host cell line” is a host cell line derived from a cell which normally expresses a particular proteinaceous molecule (or class of proteinaceous molecules) in the organism from which the cell is derived.

Heterologous STAR Sequence

The term “heterologous STAR sequence” is herein used to define a STAR sequence that is, for example, obtained from a different cell type (from the same species or organism) or is obtained from a different species or organism (either from the same cell type or a different cell type) compared to the cell in which it is used.

Stable

“Stable” means that the observed transcription level is not significantly changed over at least 30 cell divisions. A stable quality is useful in situations wherein expression characteristics should be predictable over many cell divisions. Typical examples are cell lines transfected with foreign genes. Other examples are transgenic animals and plants and gene therapies. Very often, introduced expression cassettes function differently after increasing numbers of cell divisions or plant or animal generations. A stable quality preferably comprises a capacity to maintain gene transcription in subsequent generations of a transgenic plant or animal. Of course, in the case where expression is inducible, the quality comprises the quality to maintain inducibility of expression in subsequent generations of a transgenic plant or animal.

Acceptable Expression Level

An “acceptable expression level” means an acceptable expression level for commercial exploitation. Whether or not a certain expression level is acceptable for commercial exploitation often depends on the kind of proteinaceous molecule that is produced. Acceptable expression levels of different kinds of proteinaceous molecules often involve different amounts of produced proteinaceous molecule.

A STAR sequence, a collection of STAR sequences, and/or a nucleic acid comprising a STAR sequence obtainable by a method of the invention, is of course suitable for use in a method of the invention for producing a proteinaceous molecule in a cell. In one aspect, the invention, therefore, provides a method for producing a proteinaceous molecule in a cell comprising selecting a cell for its suitability for producing the proteinaceous molecule, providing a nucleic acid encoding the proteinaceous molecule with a nucleic acid comprising a STAR sequence, expressing the resulting nucleic acid in the cell and collecting the proteinaceous molecule, wherein the nucleic acid comprising a STAR sequence is obtainable by a method of the invention for identifying and obtaining a nucleic acid comprising a STAR sequence. The nucleic acid comprising a STAR sequence can be identified and obtained using at least one pattern that is representative for sequences comprising STAR activity. Preferably, the nucleic acid comprising a STAR sequence is identified and obtained using at least one pattern as depicted in Table 6 (SEQ ID NOS:177-342) or Table 7 (SEQ ID NOS:343-1072).

A cell can be selected for its suitability for producing a proteinaceous molecule in many different ways. For instance, it can be determined whether the cell is competent of nucleic acid uptake. A nucleic acid encoding a proteinaceous molecule is preferably easily introduced into the cell. Furthermore it can be determined whether the cell secretes produced proteinaceous molecule. Secreted proteinaceous molecule can usually be easily collected. Collecting proteinaceous molecules that are not secreted usually involves sacrificing at least part of a culture. This implicates separating a proteinaceous molecule of interest from other cell components, optionally starting up a new culture, etc. This is more cumbersome. Hence, in a preferred embodiment, a method of the invention is provided wherein the proteinaceous molecule is secreted by the cell.

In another preferred embodiment, a method of the invention is provided wherein the cell is selected for its capability of post-translationally modifying the proteinaceous molecule, such that the proteinaceous molecule has essentially the same properties as a naturally occurring proteinaceous molecule of the same kind. As has been explained above, different kinds of cells display different post-translational modifications. As a result, the same proteinaceous molecule can be modified differently when produced in different host cells. These differences can affect the properties of such proteinaceous molecules, such as for instance pharmaceutical properties. It is, therefore, highly preferred to select a cell which produces a proteinaceous molecule with essentially the same properties as its naturally occurring counterpart. This does not necessarily mean that the host cell has to display exactly the same kind of post-translational modifications, as long as the produced proteinaceous molecule has essentially the same properties. A proteinaceous molecule can be produced that is physically different from its natural counterpart, but which is functionally essentially the same.

In one embodiment, of the invention, however, a cell is selected for its capability of post-translationally modifying the proteinaceous molecule in essentially the same way as the proteinaceous molecule is post-translationally modified in nature.

In one aspect, the invention provides a method of the invention wherein the proteinaceous molecule comprises an affiliated proteinaceous molecule of the cell.

It is especially preferred to choose a host cell, or a cell line derived from a cell, which normally produces a proteinaceous molecule of interest in the organism from which the cell is derived. These cells are capable of carrying out post-translational modifications of their affiliated proteinaceous molecules such that the resulting proteinaceous molecule has the same kind of properties in kind, not necessarily in amount, as a proteinaceous molecule of the same kind which is normally present in the organism. Such specific cells are naturally adapted for production of the affiliated proteinaceous molecule. Apart from other activities of STAR sequences it is also possible to at least partly solve a problem of low production of proteinaceous molecules, which often occurs with such specific cells. Providing at least one STAR sequence to a nucleic acid encoding such proteinaceous molecule will enhance production (yield) of the proteinaceous molecule by the specific cell, increase the proportion of host cells with acceptable expression levels, and/or increase stability of a gene expression level.

In another preferred embodiment, a method of the invention is disclosed wherein the cell is selected for suitable growth in a suspension culture. This facilitates culturing of the cell, and collection of produced proteinaceous molecule, especially when the proteinaceous molecule is secreted into the suspension. More preferably, the cell is selected for suitable growth in a serum-free culture, since serum can contain contaminants and pathogens. Such contaminants/pathogens often have to be separated from produced proteinaceous molecule. This requires an extra step, which consumes time and chemicals, with a potential loss of produced proteinaceous molecule. Moreover, a possibility of a presence of pathogens involves a potential risk for employees. If a pathogen has been present in a culture, a produced proteinaceous molecule is not allowed to be used anymore for commercial and/or medical applications.

In yet another preferred embodiment, the cell is selected for the presence of an adenovirus Early Region 1 (E1) sequence. The presence of an adenoviral E1 sequence enhances protein production in a cell. Hence, an adenoviral E1 sequence is suitable for host cells engineered for protein production.

The invention also provides a method for producing a proteinaceous molecule comprising:

- providing a host cell with a nucleic acid comprising a STAR sequence;
- selecting a cell with enhanced expression of a proteinaceous molecule; and
- collecting the proteinaceous molecule.

In one embodiment, the method is performed with a host cell whose genome has not been modified by human interference. The method then results in enhanced expression of a proteinaceous molecule which is encoded by the genome of the host cell. The proteinaceous molecule may be normally expressed by the host cell in the organism from which the cell is derived, but it may also normally be subject to silencing, resulting in little or no expression in the host cell under normal conditions. Introduction of at least one STAR sequence can at least in part inhibit silencing of a gene of interest induced by gene-transcription repressing chromatin. Expression of a proteinaceous molecule is enhanced by introduction of a STAR sequence.

In another embodiment, the host cell is transfected with a nucleic acid of interest. Such nucleic acid for instance, encodes a heterologous proteinaceous molecule which is not naturally encoded by the genome of the host cell. Introduction of a STAR sequence also enhances expression of such heterologous proteinaceous molecule.

The STAR sequence can be introduced randomly into the genome of the host cell, using methods known in the art (for instance calcium precipitation, transfection with a vector comprising a nucleic acid of interest, use of a gene delivery vehicle, etc). If a STAR sequence is introduced near a nucleic acid sequence encoding a proteinaceous molecule, it is capable of enhancing expression of the proteinaceous molecule. Cells expressing a desired proteinaceous molecule can be isolated from cultures with randomly inserted STAR sequences.

Preferably, the STAR sequence is introduced into the host cell by homologous recombination. A nucleic acid comprising a STAR sequence can be provided with an additional sequence. The additional sequence can be chosen such that it is at least in part homologous to a nucleic acid sequence in the host cell which is known to be present in vicinity of a gene encoding a proteinaceous molecule of interest. If a nucleic acid comprising a STAR sequence and such additional sequence is provided to the host cell, it can be incorporated into the host cell's genome by homologous recombination at the site with the (partly) homologous nucleic acid sequence. As a result, the STAR sequence is introduced in vicinity of the gene encoding the proteinaceous molecule of interest. Expression of the proteinaceous molecule is then enhanced by the introduced STAR sequence.

A preferred embodiment of the present invention provides a method of the invention wherein the STAR sequence comprises a species-specific STAR sequence. More preferably, the STAR sequence comprises a cell type-specific STAR sequence.

Two types of STAR elements have been identified. Promiscuous STAR elements are able to function in more than one host cell line. For example, STAR6 (SEQ ID NO:6) increases the predictability, yield, and stability of a transgene in both the U-2 OS human osteosarcoma cell line and in CHO (Chinese hamster ovary) cells. Other STAR elements are species-specific and/or cell type-specific; for example, STAR8 (SEQ ID NO:8) increases the predictability, yield, and stability of transgenes in U-2 OS cells, but not in CHO cells (see Examples 2 and 3 and FIGS. 3 and 4).

If a certain type of host cell (line) is chosen for expression of a proteinaceous molecule (for instance, because it is known to possess a preferred post-translational modification system) a STAR sequence which is naturally present in the cell can be used in a method of the invention. Such STAR sequence is referred to as a cell type-specific STAR sequence. A STAR sequence which is naturally present in a species from which the cell is derived can also be used. Such STAR sequence is referred to as a species-specific STAR sequence. A species-specific STAR sequence may be naturally present in the cell type, although this is not necessary.

A known species-specific STAR sequence or cell-type specific STAR sequence can be used in a method of the invention. Alternatively, a (previously unknown) species-specific STAR sequence or cell-type specific STAR sequence can be detected and isolated by a method as described by the present inventors (EP 01202581.3). The use of a species-specific STAR sequence or cell type-specific STAR sequence is preferred because such sequence is especially active in the host cell and is adapted to the specific circumstances within the cell. For instance, such cell type-specific STAR sequence may interact with a protein which is not present in some other cell-types. In that case, the cell type-specific STAR sequence will be less capable—if at all—of enhancing expression in cells lacking the protein. A species-specific or cell type-specific STAR element often has functional characteristics that are superior to promiscuous STAR elements. Furthermore, a cell line-specific STAR element can satisfy product safety or ethical considerations for use of the host cell line.

A promiscuous STAR sequence is particularly useful if no tissue specific or cell-type specific STAR sequence is known. In that case a known promiscuous STAR sequence can be used. This saves efforts to detect and isolate a cell-type specific STAR sequence.

Several STAR sequences are listed in SEQ ID NOS:1-119. Hence, in one aspect, a method of the invention is provided wherein the STAR sequence comprises a sequence as depicted in SEQ ID NOS:1-119.

In a preferred embodiment, the invention provides a cell line that comprises at least one heterologous STAR sequence or a functional equivalent and/or a functional fragment thereof. In an even more preferred embodiment, the cell line is a human cell line. The invention provides multiple examples of STAR sequences and also methods of testing STAR sequences and hence, a person skilled in the art is very well capable of obtaining a functional equivalent and/or a functional fragment of a STAR sequence, for example by deletion or mutation. In yet another preferred embodiment, the invention provides a non-human cell line that comprises at least one recombinant STAR sequence derived or obtained from a human cell, i.e., a human STAR sequence. It is clear that the amount of STAR sequences may vary, for example, a cell line according to the invention may comprise two, three, or four, or even more STAR sequences which may either be identical or different from each other.

In one aspect, the invention provides a cell line provided with a nucleic acid comprising a STAR sequence, wherein the cell line is selected for its suitability for producing a proteinaceous molecule. Preferably, a cell line of the invention comprises a vertebrate or plant cell line. A vertebrate cell line is very suitable for producing a human proteinaceous molecule of interest, because vertebrates are phylogenetically close related.

Plant cells are for instance very suitable for vaccine production. Vaccine production in plants can be inexpensive, while the vaccine can be easily delivered to an individual by eating the edible portion of the plant (Mercenier et al., 2001).

A cell line of the invention is particularly suitable for production of a proteinaceous molecule of interest, because the STAR sequence can enhance expression of a gene of interest (higher yield of a proteinaceous molecule, higher proportion of host cells with acceptable expression levels, and/or higher stability of a gene expression level). Methods for generating a cell line are known in the art and many techniques are known to provide a cell with a nucleic acid of interest. Furthermore, many general purpose cell lines are available. Such cell lines can be dedicated to production of a certain proteinaceous molecule using recombinant techniques. Examples of available cell lines include CHO cells from Chinese hamster ovary and BHK cells from baby hamster kidney (as described above).

Another embodiment of the invention provides a cell line provided with a nucleic acid comprising a STAR sequence, wherein the cell line comprises an adenovirus Early Region 1 sequence. As has been described above, an adenoviral E1 sequence enhances cellular protein production. More preferably a cell line of the invention is provided wherein the cell line comprises a U-2 OS osteosarcoma, CHO, 293, HuNS-1 myeloma, WERI-Rb-1 retinoblastoma, BHK, Vero, non-secreting mouse myeloma Sp2/0-Ag 14, non-secreting mouse myeloma NSO, or NCI-H295R adrenal gland carcinoma (ATCC CRL-2128) cell line.

A cell line of the invention is particularly suitable for production of a proteinaceous molecule, because production can be enhanced by one or more STAR sequences (higher yield of a proteinaceous molecule, higher proportion of host cells with acceptable expression levels, and/or higher stability of a gene expression level). A cell line of the invention can comprise promiscuous, species-specific and/or cell type-specific STAR sequences. Furthermore, a cell line of the invention can be used to produce a heterologous proteinaceous molecule, and/or an affiliated proteinaceous molecule.

Hence, a use of a cell line of the invention for the production of a proteinaceous molecule is also herewith provided. Preferably, the proteinaceous molecule comprises an affiliated protein of the cell line.

Of course, a proteinaceous molecule obtainable by a method of the invention is also provided by the present invention.

In one aspect, the invention provides a method for selecting a cell suitable for producing a proteinaceous molecule comprising:

- providing a nucleic acid encoding the proteinaceous molecule with a nucleic acid comprising a STAR sequence;
- expressing the resulting nucleic acid in the cell; and
- determining whether produced proteinaceous molecule has a desired property.

The desired property, for instance, comprises a pharmaceutical property. The property can be influenced by post translational modification(s), a configuration of a produced proteinaceous molecule, etc.

In yet another aspect, the invention provides a method for selecting a cell suitable for producing a proteinaceous molecule comprising:

- providing a host cell with a nucleic acid comprising a STAR sequence;
- selecting a cell with enhanced expression of a proteinaceous molecule; and
- determining whether the proteinaceous molecule has a desired property.

As has been discussed above, the nucleic acid comprising a STAR sequence can be randomly introduced into the genome of the host cell. Preferably, however, the nucleic acid sequence is introduced into the genome of the host cell by homologous recombination.

The invention is further explained in the following examples. The examples do not limit the invention in any way. They merely serve to clarify the invention.

EXAMPLES Example 1 Method for Isolation of Star Elements from the Human Genome

STAR elements are identified and cloned from human genomic DNA based on their ability to block the spread of transcriptional repression from DNA binding sites for repressor proteins in a test vector, as described in this example. The method described in this example is applicable in principle to any mammalian cell line, for isolation of both promiscuous and cell line-specific STAR elements.

A Method to Isolate Human Star Elements Functional in U-2 Os Cell

Materials and Methods

Plasmids and strains. The selection vector for STAR elements, pSelect-SV40-zeo (“pSelect,” FIG. 1) was constructed as follows: the pREP4 vector (Invitrogen V004-50) was used as the plasmid backbone. It provides the Epstein Barr oriP origin of replication and EBNA-1 nuclear antigen for high-copy episomal replication in primate cell lines; the hygromycin resistance gene with the thymidine kinase promoter and polyadenylation site, for selection in mammalian cells; and the ampicillin resistance gene and colE1 origin of replication for maintenance in Escherichia coli. The vector contains four consecutive LexA operator sites between XbaI and NheI restriction sites (Bunker and Kingston, 1994). Embedded between the LexA operators and the NheI site is a polylinker consisting of the following restriction sites: HindIII-AscI-BamHI-AscI-HindIII. Between the NheI site and a SalI site is the zeocin resistance gene with the SV40 promoter and polyadenylation site, derived from pSV40/Zeo (Invitrogen V502-20); this is the selectable marker for the STAR screen.

Gene libraries were constructed by Sau3AI digestion of human genomic DNA, either purified from placenta (Clontech 6550-1) or carried in bacterial/P1 (BAC/PAC) artificial chromosomes. The BAC/PAC clones contain genomic DNA from the 1q12 cytogenetic region (clones RP1154H19 and RP3328E19), from the HOX cluster of homeotic genes (clones RP1167F23, RP1170019, and RP11387A1), or from human chromosome 22 (Research Genetics 96010-22). The DNAs were size-fractionated, and the 0.5-2 kb size fraction ligated into BamHI-digested pSelect vector, by standard techniques (Sambrook et al., 1989).

The construction of the host strains has been described (van der Vlag et al., 2000). Briefly, they are based on the U-2 OS human osteosarcoma cell line (American Type Culture Collection HTB-96). U-2 OS was stably transfected with the pTet-Off plasmid (Clontech K1620-A), encoding a protein chimera consisting of the Tet-repressor DNA binding domain and the VP16 transactivation domain. The cell line was subsequently stably transfected with fusion protein genes containing the LexA DNA binding domain, and the coding regions of HP1, MeCP2, or HPC2 (three Drosophila proteins that repress gene expression when tethered to DNA). The LexA-repressor genes are under control of the Tet-Off transcriptional regulatory system (Gossen and Bujard, 1992).

Library screening and STAR element characterization. The gene libraries in pSelect were transfected into U-2 OS/Tet-Off/LexA-repressor cell lines by calcium phosphate precipitation (Graham and van der Eb, 1973, Wigler et al., 1978) as recommended by the supplier of the transfection reagent (Life Technologies). Transfected cells were cultured under hygromycin selection (25 μg/ml) and tetracycline repression (doxycycline, 10 ng/ml) for one week (50% confluence). Then the doxycycline concentration was reduced to 0.1 ng/ml to induce the LexA-repressor genes, and after two days zeocin was added to 250 μg/ml. The cells are cultured for a further four to five weeks, until the control cultures (transfected with empty pSelect) were killed by the zeocin.

Zeocin-resistant colonies from the library transfection were propagated, and plasmid DNA isolated and rescued into E. coli by standard techniques (Sambrook et al., 1989). The candidate STAR elements in the rescued DNA were analyzed by restriction endonuclease mapping (Sambrook et al., 1989), and tested for STAR activity (zeocin resistance) after re-transfection to U-2 OS/Tet-Off/LexA-repressor cells and lowering the doxycycline concentration.

The human genomic DNA inserts in these plasmids were sequenced by the dideoxy method (Sanger et al., 1977) using a Beckman CEQ™2000 automated DNA sequencer, using the manufacturer's instructions. Briefly, DNA was purified from E. coli using QIAprep® Spin Miniprep and Plasmid Midi Kits (QIAGEN® 27106 and 12145, respectively). Cycle sequencing was carried out using custom oligonucleotides corresponding to the pSelect vector (primers D89 (SEQ ID NO:149) and D95 (SEQ ID NO:154); all oligonucleotides are described in Table 2), in the presence of dye terminators (CEQ™ Dye Terminator Cycle Sequencing Kit, Beckman 608000). Assembled STAR DNA sequences were located in the human genome using BLAST (Basic Local Alignment Search Tool (Altschul et al., 1990); worldwideweb.ncbi.nlm.nih.gov/BLAST/).

Results

The screens of human genomic DNA have yielded 66 STAR elements; the lengths and chromosomal locations of these elements are tabulated in SEQ ID NO:1-SEQ ID NO:66. They confer zeocin resistance on U-2 OS host cells when placed between LexA-repressor binding sites and the zeocin resistance gene. Their anti-repression activity was demonstrated both in the initial screen and upon re-transfection (demonstrating that the anti-repression activity is due to the STAR element and not to somatic acquisition of zeocin resistance). The STAR elements correspond to known and unique sequences in the human genome, as demonstrated by BLAST searches (Table 3). In some cases, the cloned element is a chimera of two unlinked genomic loci (e.g., STAR3 (SEQ ID NO:3), Table 3). They range in length from 500 to 2361 base pairs in length.

Example 2 Predictability and Yield is Improved by Promiscuous Star Elements in More than One Host Cell Line

STAR elements function to block the effect of transcriptional repression influences on transgene expression units. These repression influences can be due to heterochromatin (“position effects”) or to adjacent copies of the transgene (“repeat-induced gene silencing”). Two of the benefits of STAR elements for heterologous protein production are increased predictability of finding high-expressing primary recombinant host cells and increased yield during production cycles. These benefits are illustrated in this example.

Materials and Methods

Construction of the pSDH vectors and STAR-containing derivatives: The pSDH-Tet vector was constructed by polymerase chain reaction amplification (PCR) of the luciferase open reading frame from plasmid pREP4-HSF-Luc (van der Vlag et al., 2000) using primers C67 (SEQ ID NO:136) and C68 (SEQ ID NO:137), and insertion of the SacII/BamHI fragment into SacII/BamHI-digested pUHD10-3 (Gossen and Bujard, 1992). The luciferase expression unit was re-amplified with primers C65 (SEQ ID NO:134) and C66 (SEQ ID NO:135), and re-inserted into pUHD10-3 in order to flank it with multiple cloning sites (MCSI and MCSII). An AscI site was then introduced into MCSI by digestion with EcoRI and insertion of a linker (comprised of annealed oligonucleotides D93 (SEQ ID NO:152) and D94 (SEQ ID NO:153)). The CMV promoter was amplified from plasmid pCMV-Bsd (Invitrogen K510-01) with primers D90 (SEQ ID NO:150) and D91 (SEQ ID NO:151), and used to replace the Tet-Off promoter in pSDH-Tet by SalI/SacII digestion and ligation to create vector pSDH-CMV. The luciferase open reading frame in this vector was replaced by SEAP (Secreted Alkaline Phosphatase) as follows: vector pSDH-CMV was digested with SacII and BamHI and made blunt; the SEAP open reading frame was isolated from pSEAP-basic (Clontech 6037-1) by EcoRI/SalI digestion, made blunt and ligated into pSDH-CMV to create vector pSDH-CS. The puromycin resistance gene under control of the SV40 promoter was isolated from plasmid pBabe-Puro (Morgenstern and Land, 1990) by PCR, using primers C81 (SEQ ID NO:138) and C82 (SEQ ID NO:139). This was ligated into vector pGL3-control (BamHI site removed) (Promega E1741) digested with NcoI/XbaI to create pGL3-puro. pGL3-puro was digested with BglII/SalI to isolate the SV40-puro resistance unit, which was made blunt and ligated into NheI digested, blunt-ended pSDH-CS. The resulting vector, pSDH-CSP, is shown in FIG. 2. All cloning steps were carried out following the instructions provided by the manufacturers of the reagents used, according to methods known in the art (Sambrook et al., 1989).

STAR elements were inserted into MCSI and MCSII in two steps, by digestion of the STAR element and the pSDH-CSP vector with an appropriate restriction enzyme, followed by ligation. The orientation of STAR elements in recombinant pSDH vectors was determined by restriction mapping, and in all cases verified by DNA sequence analysis using primers C85 (SEQ ID NO:140), E42 (SEQ ID NO:168), and E25 (SEQ ID NO:167) (Table 2; see Example 1).

Transfection and culture of U-2 OS cells with pSDH-CMV plasmids: The human osteosarcoma U-2 OS cell line (ATCC #HTB-96) was cultured in Dulbecco's Modified Eagle Medium+10% Fetal Calf Serum containing glutamine, penicillin, and streptomycin (supra) at 37° C./5% CO₂. Cells were co-transfected with the pSDH-CMV vector and its derivatives containing STAR6 (SEQ ID NO:6) or STAR8 (SEQ ID NO:8) in MCSI and MCSII (along with plasmid pBabe-Puro) using SuperFect® (supra). Puromycin selection was complete in two weeks, after which time individual puromycin resistant U-2 OS/pSDH-CMV clones were isolated at random and cultured further.

Luciferase assay: Luciferase activity (Himes and Shannon, 2000) was assayed in resuspended cells according to the instructions of the assay kit manufacturer (Roche 1669893), using a luminometer (Turner 20/20TD). Total cellular protein concentration was determined by the bicinchoninic acid method according to the manufacturer's instructions (Sigma B-9643), and used to normalize the luciferase data.

Transfection and culture of CHO cells with pSDH-CSP plasmids: The Chinese Hamster Ovary cell line CHO-K1 (ATCC CCL-61) was cultured in HAMS-F12 medium+10% Fetal Calf Serum containing 2 mM glutamine, 100 U/ml penicillin, and 100 micrograms/ml streptomycin at 37° C./5% CO₂. Cells were transfected with recombinant pSDH-CSP vectors using SuperFect® (QIAGEN®) as described by the manufacturer. Briefly, cells were seeded to culture vessels and grown overnight to 70-90% confluence. SuperFect® reagent was combined with plasmid DNA (linearized in this example by digestion with PvuI) at a ratio of 6 microliters per microgram (e.g., for a 10 cm Petri dish, 20 micrograms DNA and 120 microliters SuperFect®) and added to the cells. After overnight incubation, the transfection mixture was replaced with fresh medium, and the transfected cells were incubated further. After overnight cultivation, 5 micrograms/ml puromycin was added. Puromycin selection was complete in two weeks, after which time individual puromycin resistant CHO/pSDH-CSP clones were isolated at random and cultured further.

Secreted Alkaline Phosphatase (SEAP) assay: SEAP activity (Berger et al., 1988, Henthorn et al., 1988, Kain, 1997, Yang et al., 1997) in the culture medium of CHO/pSDH-CSP clones was determined as described by the manufacturer (Clontech Great EscAPe kit #K2041). Briefly, an aliquot of medium was heat inactivated at 65° C., then combined with assay buffer and CSPD chemiluminescent substrate and incubated at room temperature for ten minutes. The rate of substrate conversion was then determined in a luminometer (Turner 20/20TD). Cell density was determined by counting trypsinized cells in a Coulter ACT10 cell counter. Luminescence units were converted into picograms SEAP based on a SEAP positive control calibration curve, and normalized to cell number.

Results

Recombinant U-2 OS cell clones containing the pSDH-CMV vector, or a pSDH-CMV plasmid containing STAR6 (SEQ ID NO:6) (Table 3), were cultured for three weeks. The luciferase activity in the host cells was then determined, and is expressed as relative luciferase units (FIG. 3), normalized to total cell protein. The recombinant U-2 OS clones with STAR6 (SEQ ID NO:6) flanking the expression units had higher yields than the STAR-less clones: the STAR6 clones had maximal luciferase expression levels five-fold higher than the STAR-less clones. The STAR6 (SEQ ID NO:6) element conferred greater predictability as well: 15-20% of the clones expressed luciferase at levels comparable to or greater than the STAR-less clone with the highest expression level.

Recombinant CHO cell clones containing the pSDH-CSP vector, or a pSDH-CSP plasmid containing STAR6 (SEQ ID NO:6), were cultured for three weeks. The SEAP activity in the culture supernatants was then determined, and is expressed on the basis of cell number (FIG. 4). As can be seen, clones with the STAR6 (SEQ ID NO:6) element in the expression units were isolated that express two- to three-fold higher SEAP activity than clones whose expression units do not include this STAR element. Furthermore, the number of STAR6-containing (SEQ ID NO:6-containing) clones that express SEAP activity at or above the maximal activity of the STAR-less clones is quite high: 40% of the STAR6 clone populations exceed the highest SEAP expression of the pSDH-CSP clones.

These results demonstrate that, when used with the strong CMV promoter, the STAR6 (SEQ ID NO:6) element increases the yield of this heterologous protein in both of the host cell lines tested. STAR6 (SEQ ID NO:6) also confers increased predictability, as manifested by the large proportion of the clones with yields equal to or greater than the highest yield displayed by the STAR-less clones. Thus, STAR6 (SEQ ID NO:6) is an example of a promiscuous STAR element, able to suppress transgene repression in more than one host cell line. The cell lines used are derived from different species (human and hamster) and different tissue types (bone and ovary), reflecting the broad range of host cells in which this STAR element can be utilized in improving heterologous protein expression.

Example 3 STAR8 (SEQ ID NO:8) is a Cell Line-Specific STAR Element

The patterns of gene expression and epigenetic gene regulation in a host cell line reflect the developmental state of the somatic cells from which they are derived. Furthermore, the biotechnology industry takes advantage of general purpose cell lines from different species according to specific requirements of a heterologous protein production process. Therefore, it is expected that some STAR elements will not function in cell lines other than those in which they are isolated. This expectation has been fulfilled by some of the STAR elements shown in Table 3. One example will be given here.

Materials and Methods

pSDH vector construction, transfection and cultivation of CHO and U-2 OS cell lines, and assay methods for the SEAP and luciferase reporter genes has been described in Example 2.

Results

Recombinant U-2 OS cell clones containing the pSDH-CMV vector, or a pSDH-CMV plasmid containing STAR8 (SEQ ID NO:8) (Table 3), were cultured for three weeks. The luciferase activity in the host cells was then determined, and is expressed as relative luciferase units (FIG. 3), normalized to total cell protein. The recombinant U-2 OS clones with the STAR8 (SEQ ID NO:8) element flanking the expression units had higher yields than the STAR-less clones: the highest expression observed from STAR8 clones was two- to three-fold higher than the expression from STAR-less clones. The STAR8 (SEQ ID NO:8) element conferred greater predictability as well: for this STAR element, ˜15% of the clones displayed luciferase expression at levels comparable to or greater than the STAR-less clone with the highest expression level.

Recombinant CHO cell clones transfected with the pSDH-CSP vector, or a pSDH-CSP plasmid containing STAR8 (SEQ ID NO:8), were cultured for three weeks. The SEAP activity in the culture supernatants was then determined, and is expressed on the basis of cell number (FIG. 4). As can be seen, one clone with the STAR8 (SEQ ID NO:8) element in the expression unit had a yield approximately two-fold higher than the highest-expressing STAR-less clone. However, the rest of the STAR8 clones expressed very poorly relative to the STAR-less clone population. Since only one individual in the STAR8 population had a good yield, it is probable that the expression unit in this clone was integrated in open, transcriptionally active chromatin, and the high yield does not reflect anti-repression activity of STAR8 (SEQ ID NO:8) in CHO cells. Certainly in the CHO clones transfected with STAR8-containing (SEQ ID NO:8-containing) expression units the predictability is quite poor; of the 17 puromycin-resistant clones, only one clone had a yield of SEAP activity above the background level of expression.

This example demonstrates that good performance of a STAR element in one cell line (in this case, the U-2 OS cell line in which STAR8 (SEQ ID NO:8) was originally isolated) is not an accurate predictor of its performance in other cell lines. STAR8 (SEQ ID NO:8) is thus an example of a cell line-specific STAR element.

Example 4 STAR Elements Functionality in Diverse Cell Line

Materials and Methods

Cell lines including the U-2 OS osteosarcoma and CHO (Chinese hamster ovary) cell lines (supra), the 293 cell line (ATCC CRL-1573) derived from human embryonal kidney (immortalized by adenovirus 5 transfection), the HuNS-1 myeloma (ATCC CRL-8644) and the WERI-Rb-1 retinoblastoma cell line (ATCC HTB-169), the NCI-H295R adrenal gland carcinoma (ATCC CRL-2128), and the non-secreting mouse myelomas Sp2/0-Ag 14 and NSO are examined according to the previous examples.

Example 5 STAR Elements Improve the Stability of Transgene Expression

During cultivation of recombinant host cells, it is common practice to maintain antibiotic selection. This is intended to prevent transcriptional silencing of the transgene, or loss of the transgene from the genome by processes such as recombination. However it is undesirable for production of heterologous proteins, for a number of reasons. First, the antibiotics that are used are quite expensive, and contribute significantly to the unit cost of the product. Second, for biopharmaceutical use, the protein must be demonstrably pure, with no traces of the antibiotic in the product. One advantage of STAR elements for heterologous protein production is that they confer stable expression on transgenes during prolonged cultivation, even in the absence of antibiotic selection; this property is demonstrated in this example.

Materials and Methods

The U-2 OS cell line was transfected with the plasmid pSDH-Tet-STAR6 and cultivated as described in Example 2. Individual puromycin-resistant clones were isolated and cultivated further in the absence of doxycycline. At weekly intervals the cells were transferred to fresh culture vessels at a dilution of 1:20. Luciferase activity was measured at periodic intervals as described in Example 2. After 15 weeks, the cultures were divided into two replicates; one replicate continued to receive puromycin, while the other replicate received no antibiotic for the remainder of the experiment (25 weeks total).

Results

Table 4 presents the data on luciferase expression by an expression unit flanked with STAR6 (SEQ ID NO:6) during prolonged growth with or without antibiotic. As can be seen, the expression of the reporter transgene, luciferase, remains stable in the U-2 OS host cells for the duration of the experiment. After the cultures were divided into two treatments (plus antibiotic and without antibiotic) the expression of luciferase was essentially stable in the absence of antibiotic selection. This demonstrates the ability of STAR elements to protect transgenes from silencing or loss during prolonged cultivation. It also demonstrates that this property is independent of antibiotic selection. Therefore, production of heterologous proteins is possible without incurring the costs of the antibiotic or of difficult downstream processing.

Example 6 Minimal Essential Sequences of STAR Elements

STAR elements are isolated from the genetic screen described in Example 1. The screen uses libraries constructed with human genomic DNA that was size-fractionated to approximately 0.5-2 kilobases (supra). The STAR elements range from 500 to 2361 base pairs (Table 3). It is likely that, for many of the STAR elements that have been isolated, STAR activity is conferred by a smaller DNA fragment than the initially isolated clone. It is useful to determine these minimum fragment sizes that are essential for STAR activity, for two reasons. First, smaller functional STAR elements would be advantageous in the design of compact expression vectors, since smaller vectors transfect host cells with higher efficiency. Second, determining minimum essential STAR sequences permits the modification of those sequences for enhanced functionality. Two STAR elements have been fine-mapped to determine their minimal essential sequences.

Materials and Methods

STAR10 (SEQ ID NO:10) (1167 base pairs) and STAR27 (SEQ ID NO:27) (1520 base pairs) have been fine-mapped. They have been amplified by PCR to yield sub-fragments of approximately equal length (FIG. 6 legend). For initial testing, these have been cloned into the pSelect vector at the BamHI site, and transfected into U-2 OS/Tet-Off/LexA-HP1 cells as described in Example 1. After selection for hygromycin resistance, LexA-HP1 was induced by lowering the doxycycline concentration. Transfected cells were then incubated with zeocin to test the ability of the STAR fragments to protect the SV40-Zeo expression unit from repression due to LexA-HP1 binding.

Results

In this experiment STAR10 (SEQ ID NO:10) and STAR 27 (SEQ ID NO:27) confer good protection against gene silencing, as expected (FIG. 6). This is manifested by robust growth in the presence of zeocin.

Of the three STAR10 (SEQ ID NO:10) sub-fragments, 10A (˜400 base pairs, corresponding to approximately the first 400 nucleotides of SEQ ID NO:10) confers on transfected cells vigorous growth in the presence of zeocin, exceeding that of the full-length STAR element. Cells transfected with pSelect constructs containing the other two sub-fragments do not grow in the presence of zeocin. These results identify the ˜400 base pair 10A fragment as encompassing the DNA sequence responsible for the anti-repression activity of STAR10 (SEQ ID NO:10).

STAR27 (SEQ ID NO:27) confers moderate growth in zeocin to transfected cells in this experiment (FIG. 6). One of the sub-fragments of this STAR, 27B (˜500 base pairs, corresponding to approximately the second 500 nucleotides of SEQ ID NO:27), permits weak growth of the host cells in zeocin-containing medium. This suggests that the anti-repression activity of this STAR is partially localized on sub-fragment 27B, but full activity requires sequences from 27A (corresponding to approximately the first 500 nucleotides of SEQ ID NO:27) and/or 27C (corresponding to approximately the third 500 nucleotides of SEQ ID NO:27) (each ˜500 base pairs) as well.

Example 7 STAR Elements Function in the Context of Various Transcriptional Promoters

Transgene transcription is achieved by placing the transgene open reading frame under control of an exogenous promoter. The choice of promoter is influenced by the nature of the heterologous protein and the production system. In most cases, strong constitutive promoters are preferred because of the high yields they can provide. Some viral promoters have these properties; the promoter/enhancer of the cytomegalovirus immediate early gene (“CMV promoter”) is generally regarded as the strongest promoter in common biotechnological use (Boshart et al., 1985, Doll et al., 1996, Foecking and Hofstetter, 1986). The simian virus SV40 promoter is also moderately strong (Boshart et al., 1985, Foecking and Hofstetter, 1986) and is frequently used for ectopic expression in mammalian cell vectors. The Tet-Off promoter is inducible: the promoter is repressed in the presence of tetracycline or related antibiotics (doxycycline is commonly used) in cell-lines which express the tTA plasmid (Clontech K1620-A), and removal of the antibiotic results in transcriptional induction (Deuschle et al., 1995, Gossen and Bujard, 1992, Izumi and Gilbert, 1999, Umana et al., 1999).

Materials and Methods

The construction of the pSDH-Tet and pSDH-CMV vectors is described in Example 2. pSDH-SV40 was constructed by PCR amplification of the SV40 promoter (primers D41 (SEQ ID NO:142) and D42 (SEQ ID NO:143)) from plasmid pSelect-SV40-Zeo (Example 1), followed by digestion of the PCR product with SacII and SalI. The pSDH-CMV vector was digested with SacII and SalI to remove the CMV promoter, and the vector and SV40 fragment were ligated together to create pSDH-SV40. STAR6 (SEQ ID NO:6) was cloned into MCSI and MCSII as described in Example 2. The plasmids pSDH-Tet, pSDH-Tet-STAR6, pSDH-Tet-STAR7, pSDH-SV40 and pSDH-SV40-STAR6 were co-transfected with pBabe-Puro into U-2 OS using SuperFect® as described by the manufacturer. Cell cultivation, puromycin selection, and luciferase assays were carried out as described in Example 2.

Results

FIGS. 3, 7, and 8 compare the expression of the luciferase reporter gene from three different promoters: two strong and constitutive viral promoters (CMV and SV40), and the inducible Tet-Off promoter. All three promoters were tested in the context of the STAR6 (SEQ ID NO:6) element in U-2 OS cells. The results demonstrate that the yield and predictability from all three promoters are increased by STAR6 (SEQ ID NO:6). As described in Examples 2 and 5, STAR6 (SEQ ID NO:6) is beneficial in the context of the CMV promoter (FIG. 3). Similar improvements are seen in the context of the SV40 promoter (FIG. 7): the yield from the highest-expressing STAR6 clone is two- to three-fold greater than the best pSDH-SV40 clones, and six STAR clones (20% of the population) have yields higher than the best STAR-less clones. In the context of the Tet-Off promoter under inducing (low doxycycline) concentrations, STAR6 (SEQ ID NO:6) also improves the yield and predictability of transgene expression (FIG. 8): the highest-expressing STAR6 clone has a 20-fold higher yield than the best pSDH-Tet clone, and nine STAR6 clones (35% of the population) have yields higher than the best STAR-less clone. It is concluded that this STAR element is versatile in its transgene-protecting properties, since it functions in the context of various biotechnologically useful promoters of transcription.

Example 8 STAR Element Function can be Directional

While short nucleic acid sequences can be symmetrical (e.g., palindromic), longer, naturally-occurring sequences are typically asymmetrical. As a result, the information content of nucleic acid sequences is directional and the sequences themselves can be described with respect to their 5′ and 3′ ends. The directionality of nucleic acid sequence information affects the arrangement in which recombinant DNA molecules are assembled using standard cloning techniques known in the art (Sambrook et al., 1989). STAR elements are long, asymmetrical DNA sequences, and have a directionality based on the orientation in which they were originally cloned in the pSelect vector. In the examples given above, using two STAR elements in pSDH vectors, this directionality was preserved. This orientation is described as the native or 5′-3′ orientation, relative to the zeocin resistance gene (see FIG. 9). In this example the importance of directionality for STAR function is tested in the pSDH-Tet vector. Since the reporter genes in the pSDH vectors are flanked on both sides by copies of the STAR element of interest, the orientation of each STAR copy must be considered. This example compares the native orientation with the opposite orientation (FIG. 9).

Materials and Methods

The STAR66 (SEQ ID NO:66) element was cloned into pSDH-Tet as described in Example 2. U-2 OS cells were co-transfected with plasmids pSDH-Tet-STAR66-native and pSDH-Tet-STAR66-opposite, and cultivated as described in Example 2. Individual clones were isolated and cultivated; the level of luciferase expression was determined as described (supra).

Results

The results of the comparison of STAR66 (SEQ ID NO:66) activity in the native orientation and the opposite orientation are shown in FIG. 10. When STAR66 (SEQ ID NO:66) is in the opposite orientation, the yield of only one clone is reasonably high (60 luciferase units). In contrast, the yield of the highest-expressing clone when STAR66 (SEQ ID NO:66) is in the native orientation is considerably higher (100 luciferase units) and the predictability is much higher, as well: seven clones of the native-orientation population (30%) express luciferase above the level of the highest-expressing clone from the opposite-orientation population, and 15 of the clones in the native-orientation population (60%) express luciferase above ten relative luciferase units. Therefore, it is demonstrated that STAR66 (SEQ ID NO:66) function is directional.

Example 9 Transgene Expression in the Context of STAR Elements is Copy Number-Dependent

Transgene expression units for heterologous protein expression are generally integrated into the genome of the host cell to ensure stable retention during cell division. Integration can result in one or multiple copies of the expression unit being inserted into the genome; multiple copies may or may not be present as tandem arrays. The increased yield demonstrated for transgenes protected by STAR elements (supra) suggests that STAR elements are able to permit the transgene expression units to function independently of influences on transcription associated with the site of integration in the genome (independence from position effects (Boivin and Dura, 1998)). It suggests further that the STAR elements permit each expression unit to function independently of neighboring copies of the expression unit when they are integrated as a tandem array (independence from repeat-induced gene silencing (Garrick et al., 1998)). Copy number-dependence is determined from the relationship between transgene expression levels and copy number, as described in the example below.

Materials and Methods

U-2 OS cells were co-transfected with pSDH-Tet-STAR10 and cultivated under puromycin selection as described (supra). Eight individual clones were isolated and cultivated further. Then cells were harvested, and one portion was assayed for luciferase activity as described (supra). The remaining cells were lysed and the genomic DNA purified using the DNeasy® Tissue Kit (QIAGEN® 69504) as described by the manufacturer. DNA samples were quantitated by UV spectrophotometry. Three micrograms of each genomic DNA sample were digested with PvuII and XhoI overnight as described by the manufacturer (New England Biolabs), and resolved by agarose gel electrophoresis. DNA fragments were transferred to a nylon membrane as described (Sambrook et al., 1989), and hybridized with a radioactively labeled probe to the luciferase gene (isolated from BamHI/SacII-digested pSDH-Tet). The blot was washed as described (Sambrook et al., 1989) and exposed to a phosphorimager screen (Personal F/X, BioRad). The resulting autoradiogram (FIG. 11) was analyzed by densitometry to determine the relative strength of the luciferase DNA bands, which represents the transgene copy number.

Results

The enzyme activities and copy numbers (DNA band intensities) of luciferase in the clones from the pSDH-Tet-STAR10 clone population is shown in FIG. 12. The transgene copy number is highly correlated with the level of luciferase expression in these pSDH-Tet-STAR10 clones (r=0.86). This suggests that STAR10 (SEQ ID NO:10) confers copy number-dependence on the transgene expression units, making transgene expression independent of other transgene copies in tandem arrays and independent of gene-silencing influences at the site of integration.

Example 10 STAR Elements Function as Enhancer Blockers but not Enhancers

Gene promoters are subject to both positive and negative influences on their ability to initiate transcription. An important class of elements that exert positive influences are enhancers. Enhancers are characteristically able to affect promoters even when they are located far away (many kilobase pairs) from the promoter. Negative influences that act by heterochromatin formation (e.g., Polycomb group proteins) have been described above, and these are the target of STAR activity. The biochemical basis for enhancer function and for heterochromatin formation is fundamentally similar, since they both involve binding of proteins to DNA. Therefore, it is important to determine whether STAR elements are able to block positive influences as well as negative influences, in other words, to shield transgenes from genomic enhancers in the vicinity of the site of integration. The ability to shield transgenes from enhancer activity ensures stable and predictable performance of transgenes in biotechnological applications. This example examines the performance of STAR elements in an enhancer-blocking assay.

Another feature of STAR activity that is important to their function is the increased yield they confer on transgenes (Example 2). STARs are isolated on the basis of their ability to maintain high levels of zeocin expression when heterochromatin-forming proteins are bound adjacent to the candidate STAR elements. High expression is predicted to occur because STARs are anticipated to block the spread of heterochromatin into the zeocin expression unit. However, a second scenario is that the DNA fragments in zeocin-resistant clones contain enhancers. Enhancers have been demonstrated to have the ability to overcome the repressive effects of Polycomb-group proteins such as those used in the method of the STAR screen (Zink and Paro, 1995). Enhancers isolated by this phenomenon would be considered false positives, since enhancers do not have the properties claimed here for STARs. In order to demonstrate that STAR elements are not enhancers, they have been tested in an enhancer assay.

The enhancer-blocking assay and the enhancer assay are methodologically and conceptually similar. The assays are shown schematically in FIG. 13. The ability of STAR elements to block enhancers is performed using the E47/E-box enhancer system. The E47 protein is able to activate transcription by promoters when it is bound to an E-box DNA sequence located in the vicinity of those promoters (Quong et al., 2002). E47 is normally involved in regulation of B and T lymphocyte differentiation (Quong et al., 2002), but it is able to function in diverse cell types when expressed ectopically (Petersson et al., 2002). The E-box is a palindromic DNA sequence, CANNTG (Knofler et al., 2002). In the enhancer-blocking assay, an E-box is placed upstream of a luciferase reporter gene (including a minimal promoter) in an expression vector. A cloning site for STAR elements is placed between the E-box and the promoter. The E47 protein is encoded on a second plasmid. The assay is performed by transfecting both the E47 plasmid and the luciferase expression vector into cells; the E47 protein is expressed and binds to the E-box, and the E47/E-box complex is able to act as an enhancer. When the luciferase expression vector does not contain a STAR element, the E47/E-box complex enhances luciferase expression (FIG. 13A, situation 1). When STAR elements are inserted between the E-box and the promoter, their ability to block the enhancer is demonstrated by reduced expression of luciferase activity (FIG. 13A, situation 2); if STARs cannot block enhancers, luciferase expression is activated (FIG. 13A, situation 3).

The ability of STAR elements to act as enhancers utilizes the same luciferase expression vector. In the absence of E47, the E-box itself does not affect transcription. Instead, enhancer behavior by STAR elements will result in activation of luciferase transcription. The assay is performed by transfecting the luciferase expression vector without the E47 plasmid. When the expression vector does not contain STAR elements, luciferase expression is low (FIG. 13B, situation 1). If STAR elements do not have enhancer properties, luciferase expression is low when a STAR element is present in the vector (FIG. 13B, situation 2). If STAR elements do have enhancer properties, luciferase expression will be activated in the STAR-containing vectors (FIG. 13B, situation 3).

Materials and Methods

The luciferase expression vector was constructed by inserting the E-box and a human alkaline phosphatase minimal promoter from plasmid mu-E5+E2×6-cat(x) (Ruezinsky et al., 1991) upstream of the luciferase gene in plasmid pGL3-basic (Promega E1751), to create pGL3-E-box-luciferase (gift of W. Romanow). The E47 expression plasmid contains the E47 open reading frame under control of a beta-actin promoter in the pHBAPr-1-neo plasmid; E47 in constitutively expressed from this plasmid (gift of W. Romanow).

STAR elements

1, 2, 3, 6, 10, 11, 18, and 27 (SEQ ID NOS:1, 2, 3, 6, 10, 11, 18, and 27, respectively) have been cloned into the luciferase expression vector. Clones containing the Drosophila scs element and the chicken beta-globin HS4-6× core (“HS4”) element have been included as positive controls (they are known to block enhancers, and to have no intrinsic enhancer properties (Chung et al., 1993, Kellum and Schedl, 1992)), and the empty luciferase expression vector has been included as a negative control. All assays were performed using the U-2 OS cell line. In the enhancer-blocking assay, the E47 plasmid was co-transfected with the luciferase expression vectors (empty vector, or containing STAR or positive-control elements). In the enhancer assay, the E47 plasmid was co-transfected with STARless luciferase expression vector as a positive control for enhancer activity; all other samples received a mock plasmid during co-transfection. The transiently transfected cells were assayed for luciferase activity 48 hours after plasmid transfection (supra). The luciferase activity expressed from a plasmid containing no E-box or STAR/control elements was subtracted, and the luciferase activities were normalized to protein content as described (supra).

Results

FIG. 14 shows the results of the enhancer-blocking assay. In the absence of STAR elements (or the known enhancer-blocking elements scs and HS4), the E47/E-box enhancer complex activates expression of luciferase (“vector”); this enhanced level of expression has been normalized to 100. Enhancer activity is blocked by all STAR elements tested. Enhancer activity is also blocked by the HS4 and scs elements, as expected (Bell et al., 2001, Gerasimova and Corces, 2001). These results demonstrate that in addition to their ability to block the spreading of transcriptional silencing (negative influences), STAR elements are able to block the action of enhancers (positive influences).

FIG. 15 shows the results of the enhancer assay. The level of luciferase expression due to enhancement by the E47/E-box complex is set at 100 (“E47”). By comparison, none of the STAR elements bring about significant activation of luciferase expression. As expected, the scs and HS4 elements also do not bring about activation of the reporter gene. Therefore, it is concluded that at least the tested STAR elements do not possess enhancer properties.

Example 11 Star Elements are Conserved Between Mouse and Human

BLAT analysis of the STAR DNA sequence against the human genome database (http://genome.ucsc.edu/cgi-bin/hgGateway) reveals that some of these sequences have high sequence conservation with other regions of the human genome. These duplicated regions are candidate STAR elements; if they do show STAR activity, they would be considered paralogs of the cloned STARs (two genes or genetic elements are said to be paralogous if they are derived from a duplication event (Li, 1997)).

BLAST analysis of the human STARs against the mouse genome (http://www.ensembl.org/Mus_musculus/blastview) also reveals regions of high sequence conservation between mouse and human. This sequence conservation has been shown for fragments of 15 out of the 65 human STAR elements. The conservation ranges from 64% to 89%, over lengths of 141 base pairs to 909 base pairs (Table 5). These degrees of sequence conservation are remarkable and suggest that these DNA sequences may confer STAR activity within the mouse genome as well. Some of the sequences from the mouse and human genomes in Table 5 could be strictly defined as orthologs (two genes or genetic elements are said to be orthologous if they are derived from a speciation event (Li, 1997)). For example, STAR6 (SEQ ID NO:6) is between the SLC8A1 and HAAO genes in both the human and mouse genomes. In other cases, a cloned human STAR has a paralog within the human genome, and its ortholog has been identified in the mouse genome. For example, STAR3a is a fragment of the 15q11.2 region of human chromosome 15. This region is 96.9% identical (paralogous) with a DNA fragment at 5q33.3 on human chromosome 5, which is near the IL12B interleukin gene. These human DNAs share approximately 80% identity with a fragment of the 11B2 region on mouse chromosome 11. The 11B2 fragment is also near the (mouse) IL12B interleukin gene. Therefore, STAR3a and the mouse 11B2 fragment can be strictly defined as paralogs.

In order to test the hypothesis that STAR activity is shared between regions of high sequence conservation in the mouse and human genome, one of the human STARs with a conserved sequence in mouse, STAR18 (SEQ ID NO:18), has been analyzed in greater detail. The sequence conservation in the mouse genome detected with the original STAR18 clone extends leftward on human chromosome 2 for about 500 base pairs (FIG. 16; left and right relate to the standard description of the arms of chromosome 2). In this example, we examine whether the region of sequence conservation defines a “naturally occurring” STAR element in human that is more extensive in length than the original clone. We also examine whether the STAR function of this STAR element is conserved between mouse and human.

Materials and Methods

The region of mouse/human sequence conservation around STAR18 (SEQ ID NO:18) was recovered from human BAC clone RP11-387A1 by PCR amplification, in three fragments: the entire region (primers E93 (SEQ ID NO:171) and E94 (SEQ ID NO:172)), the leftward half (primers E93 (SEQ ID NO:171) and E92 (SEQ ID NO:170)), and the rightward half (primers E57 (SEQ ID NO:169) and E94 (SEQ ID NO:172)). The corresponding fragments from the homologous mouse region were recovered from BAC clone RP23-400H17 in the same fashion (primers E95 (SEQ ID NO:173) and E98 (SEQ ID NO:176), E95 (SEQ ID NO:173) and E96 (SEQ ID NO:174), and E97 (SEQ ID NO:175) and E98 (SEQ ID NO:176), respectively). All fragments were cloned into the pSelect vector and transfected into a U-2 OS/Tet-Off/LexA-HP1 cell line (supra). Following transfection, hygromycin selection was carried out to select for transfected cells. The LexA-HP1 protein was induced by lowering the doxycycline concentration, and the ability of the transfected cells to withstand the antibiotic zeocin (a measure of STAR activity) was assessed by monitoring cell growth.

Results

The original STAR18 clone was isolated from Sau3AI digested human DNA ligated into the pSelect vector on the basis of its ability to prevent silencing of a zeocin resistance gene. Alignment of the human STAR18 clone (497 base pairs) with the mouse genome revealed high sequence similarity (72%) between the orthologous human and mouse STAR18 (SEQ ID NO:18) regions. It also uncovered high similarity (73%) in the region extending for 488 base pairs immediately to the left of the Sau3AI site that defines the left end of the cloned region (FIG. 16). Outside these regions the sequence similarity between human and mouse DNA drops below 60%.

As indicated in FIG. 16, both the human and the mouse STAR18 (SEQ ID NO:18) elements confer survival on zeocin to host cells expressing the lexA-HP1 repressor protein. The original 497 base pair STAR18 clone and its mouse ortholog both confer the ability to grow (FIG. 16, a and d). The adjacent 488 base pair regions of high similarity from both genomes also confer the ability to grow, and in fact their growth phenotype is more vigorous than that of the original STAR18 clone (FIG. 16, b and e). When the entire region of sequence similarity was tested, these DNAs from both mouse and human confer growth, and the growth phenotype is more vigorous than the two sub-fragments (FIG. 16, c and f). These results demonstrate that the STAR activity of human STAR18 (SEQ ID NO:18) is conserved in its ortholog from mouse. The high sequence conservation between these orthologous regions is particularly noteworthy because they are not protein-coding sequences, leading to the conclusion that they have some regulatory function that has prevented their evolutionary divergence through mutation.

This analysis demonstrates that cloned STAR elements identified by the original screening program may in some cases represent partial STAR elements, and that analysis of the genomic DNA in which they are embedded can identify sequences with stronger STAR activity.

Example 12 STAR Elements Contain Characteristic DNA Sequence Motifs

STAR elements are isolated on the basis of their anti-repression phenotype with respect to transgene expression. This anti-repression phenotype reflects underlying biochemical processes that regulate chromatin formation which are associated with the STAR elements. These processes are typically sequence-specific and result from protein binding or DNA structure. This suggests that STAR elements will share DNA sequence similarity. Identification of sequence similarity among STAR elements will provide sequence motifs that are characteristic of the elements that have already been identified by functional screens and tests. The sequence motifs will also be useful to recognize and claim new STAR elements whose functions conform to the claims of this patent. The functions include improved yield and stability of transgenes expressed in eukaryotic host cells.

Other benefits of identifying sequence motifs that characterize STAR elements include: (1) provision of search motifs for prediction and identification of new STAR elements in genome databases, (2) provision of a rationale for modification of the elements, and (3) provision of information for functional analysis of STAR activity. Using bio-informatics, sequence similarities among STAR elements have been identified; the results are presented in this example.

Bio-Informatic and Statistical Background

Regulatory DNA elements typically function via interaction with sequence-specific DNA-binding proteins. Bio-informatic analysis of DNA elements, such as STAR elements whose regulatory properties have been identified, but whose interacting proteins are unknown, requires a statistical approach for identification of sequence motifs. This can be achieved by a method that detects short DNA sequence patterns that are over-represented in a set of regulatory DNA elements (e.g., the STAR elements) compared to a reference sequence (e.g., the complete human genome). The method determines the number of observed and expected occurrences of the patterns in each regulatory element. The number of expected occurrences is calculated from the number of observed occurrences of each pattern in the reference sequence.

The DNA sequence patterns can be oligonucleotides of a given length, e.g., six base pairs. In the simplest analysis, for a six-base-pair oligonucleotide (hexamer) composed of the four nucleotides (A, C, G, and T) there are 4⁶=4096 distinct oligonucleotides (all combinations from AAAAAA (SEQ ID NO:121) to TTTTTT (SEQ ID NO:122)). If the regulatory and reference sequences were completely random and had equal proportions of the A, C, G, and T nucleotides, then the expected frequency of each hexamer would be 1/4096 (˜0.00024). However, the actual frequency of each hexamer in the reference sequence is typically different than this due to biases in the content of G:C base pairs, etc. Therefore, the frequency of each oligonucleotide in the reference sequence is determined empirically by counting, to create a “frequency table” for the patterns.

The pattern frequency table of the reference sequence is then used to calculate the expected frequency of occurrence of each pattern in the regulatory element set. The expected frequencies are compared with the observed frequencies of occurrence of the patterns. Patterns that are “over-represented” in the set are identified; for example, if the hexamer ACGTGA (SEQ ID NO:123) is expected to occur five times in 20 kilobase pairs of sequence, but is observed to occur 15 times, then it is three-fold over-represented. Ten of the 15 occurrences of that hexameric sequence pattern would not be expected in the regulatory elements if the elements had the same hexamer composition as the entire genome. Once the over-represented patterns are identified, a statistical test is applied to determine whether their over-representation is significant, or may be due to chance. For this test, a significance index, “sig,” is calculated for each pattern. The significance index is derived from the probability of occurrence of each pattern, which is estimated by a binomial distribution. The probability takes into account the number of possible patterns (4096 for hexamers). The highest sig values correspond to the most overrepresented oligonucleotides (van Helden et al., 1998). In practical terms, oligonucleotides with sig ≧0 are considered as over-represented. A pattern with sig ≧0 is likely to be over-represented due to chance once (=10⁰) in the set of regulatory element sequences. However, at sig ≧1 a pattern is expected to be over-represented once in ten (=10¹) sequence sets, sig ≧2 once in 100 (=10²) sequence sets, etc.

The patterns that are significantly over-represented in the regulatory element set are used to develop a model for classification and prediction of regulatory element sequences. This employs Discriminant Analysis, a so-called “supervised” method of statistical classification known to one of ordinary skill in the art (Huberty, 1994). In Discriminant Analysis, sets of known or classified items (e.g., STAR elements) are used to “train” a model to recognize those items on the basis of specific variables (e.g., sequence patterns such as hexamers). The trained model is then used to predict whether other items should be classified as belonging to the set of known items (e.g., is a DNA sequence a STAR element). In this example, the known items in the training set are STAR elements (positive training set). They are contrasted with sequences that are randomly selected from the genome (negative training set) which have the same length as the STAR elements. Discriminant Analysis establishes criteria for discriminating positives from negatives based on a set of variables that distinguish the positives; in this example, the variables are the significantly over-represented patterns (e.g., hexamers).

When the number of over-represented patterns is high compared to the size of the training set, the model could become biased due to over-training. Over-training is circumvented by applying a forward stepwise selection of variables (Huberty, 1994). The goal of Stepwise Discriminant Analysis is to select the minimum number of variables that provides maximum discrimination between the positives and negatives. The model is trained by evaluating variables one-by-one for their ability to properly classify the items in the positive and negative training sets. This is done until addition of new variables to the model does not significantly increase the model's predictive power (i.e., until the classification error rate is minimized). This optimized model is then used for testing, in order to predict whether “new” items are positives or negatives (Huberty, 1994).

It is inherent in classification statistics that for complex items such as DNA sequences, some elements of the positive training set will be classified as negatives (false negatives), and some members of the negative training set will be classified as positives (false positives). When a trained model is applied to testing new items, the same types of misclassifications are expected to occur.

In the bio-informatic method described here, the first step, Pattern Frequency Analysis, reduces a large set of sequence patterns (e.g., all 4096 hexamers) to a smaller set of significantly over-represented patterns (e.g., 100 hexamers); in the second step, Stepwise Discriminant Analysis reduces the set of over-represented patterns to the subset of those patterns that have maximal discriminative power (e.g., five to ten hexamers). Therefore, this approach provides simple and robust criteria for identifying regulatory DNA elements such as STAR elements.

DNA-binding proteins can be distinguished on the basis of the type of binding site they occupy. Some recognize contiguous sequences; for this type of protein, patterns that are oligonucleotides of length six base pairs (hexamers) are fruitful for bio-informatic analysis (van Helden et al., 1998). Other proteins bind to sequence dyads: contact is made between pairs of highly conserved trinucleotides separated by a non-conserved region of fixed width (van Helden et al., 2000). In order to identify sequences in STAR elements that may be bound by dyad-binding proteins, frequency analysis was also conducted for this type of pattern, where the spacing between the two trinucleotides was varied from 0 to 20 (i.e., XXXN{0-20}XXX where X's are specific nucleotides composing the trinucleotides, and N's are random nucleotides from 0 to 20 base pairs in length). The results of dyad frequency analysis are also used for Linear Discriminant Analysis as described above.

Materials and Methods

Using the genetic screen described in the original patent application, sixty-six (66) STAR elements were initially isolated from human genomic DNA and characterized in detail (Table 3). The screen was performed on gene libraries constructed by Sau3AI digestion of human genomic DNA, either purified from placenta (Clontech 6550-1) or carried in bacterial/P1 (BAC/PAC) artificial chromosomes. The BAC/PAC clones contain genomic DNA from regions of chromosome 1 (clones RP1154H19 and RP3328E19), from the HOX cluster of homeotic genes (clones RP1167F23, RP1170019, and RP11387A1), or from human chromosome 22 (Research Genetics 96010-22). The DNAs were size-fractionated, and the 0.5-2 kb size fraction was ligated into BamHI-digested pSelect vector, by standard techniques (Sambrook et al., 1989). pSelect plasmids containing human genomic DNA that conferred resistance to zeocin at low doxycycline concentrations were isolated and propagated in Escherichia coli. The screens that yielded the STAR elements of Table 3 have assayed approximately 1-2% of the human genome.

The human genomic DNA inserts in these 66 plasmids were sequenced by the dideoxy method (Sanger et al., 1977) using a Beckman CEQ™2000 automated DNA sequencer, using the manufacturer's instructions. Briefly, DNA was purified from E. coli using QIAprep® Spin Miniprep and Plasmid Midi Kits (QIAGEN® 27106 and 12145, respectively). Cycle sequencing was carried out using custom oligonucleotides corresponding to the pSelect vector (primers D89 (SEQ ID NO:149) and D95 (SEQ ID NO:154), Table 2), in the presence of dye terminators (CEQ™ Dye Terminator Cycle Sequencing Kit, Beckman 608000). Assembled STAR DNA sequences were located in the human genome (database builds August and December 2001) using BLAT (Basic Local Alignment Tool (Kent, 2002); http://genome.ucsc.edu/cgi-bin/hgGateway; Table 3). In aggregate, the combined STAR sequences comprise 85.6 kilobase pairs, with an average length of 1.3 kilobase pairs.

Sequence motifs that distinguish STAR elements within human genomic DNA were identified by bio-informatic analysis using a two-step procedure, as follows (see FIG. 17 for a schematic diagram). The analysis has two input datasets: (1) the DNA sequences of the STAR elements (STAR1-STAR65 (SEQ ID NOS:1-65) were used; Table 3); and (2) the DNA sequence of the human genome (except for chromosome 1, which was not feasible to include due to its large size; for dyad analysis a random subset of human genomic DNA sequence (˜27 Mb) was used).

Pattern Frequency Analysis

The first step in the analysis uses RSA-Tools software (Regulatory Sequence Analysis Tools; http://www.ucmb.ulb.ac.be/bioinformatics/rsa-tools/; references (van Helden et al., 1998, van Helden et al., 2000, van Helden et al., 2000)) to determine the following information: (1) the frequencies of all dyads and hexameric oligonucleotides in the human genome; (2) the frequencies of the oligonucleotides and dyads in the 65 STAR elements; and (3) the significance indices of those oligonucleotides and dyads that are over-represented in the STAR elements compared to the genome. A control analysis was done with 65 sequences that were selected at random from the human genome (i.e., from 2689×10³kilobase pairs) that match the length of the STAR elements of Table 3.

Discriminant Analysis

The over-represented oligonucleotides and dyads were used to train models for prediction of STAR elements by Linear Discriminant Analysis (Huberty, 1994). A pre-selection of variables was performed by selecting the 50 patterns with the highest individual discriminatory power from the over-represented oligos or dyads of the frequency analyses. These pre-selected variables were then used for model training in a Stepwise Linear Discriminant Analysis to select the most discriminant combination of variables (Huberty, 1994). Variable selection was based on minimizing the classification error rate (percentage of false negative classifications). In addition, the expected error rate was estimated by applying the same discriminant approach to the control set of random sequences (minimizing the percentage of false positive classifications).

The predictive models from the training phase of Discriminant Analysis were tested in two ways. First, the STAR elements and random sequences that were used to generate the model (the training sets) were classified. Second, sequences in a collection of 19 candidate STAR elements (recently cloned by zeocin selection as described above) were classified. These candidate STAR elements are listed in Table 8 (SEQ ID NOS:66-84).

Results

Pattern frequency analysis was performed with RSA-Tools on 65 STAR elements, using the human genome as the reference sequence. One hundred sixty-six (166) hexameric oligonucleotides were found to be over-represented in the set of STAR elements (sig ≧0) compared to the entire genome (Table 6). The most significantly over-represented oligonucleotide, CCCCAC (SEQ ID NO:177), occurs 107 times among the 65 STAR elements, but is expected to occur only 49 times. It has a significance coefficient of 8.76; in other words, the probability that its over-representation is due to random chance is 1/10^8.76, i.e., less than one in 500 million.

Ninety-five of the oligonucleotides have a significance coefficient greater than one, and are, therefore, highly over-represented in the STAR elements. Among the over-represented oligonucleotides, their observed and expected occurrences, respectively, range from 6 and 1 (for oligo 163, CGCGAA (SEQ ID NO:339), sig=0.02) to 133 and 95 (for oligo 120, CCCAGG (SEQ ID NO:296), sig=0.49). The differences in expected occurrences reflect factors such as the G:C content of the human genome. Therefore, the differences among the oligonucleotides in their number of occurrences is less important than their over-representation; for example, oligo 2 (CAGCGG (SEQ ID NO:178)) is 36/9=four-fold over-represented, which has a probability of being due to random chance of one in fifty million (sig=7.75).

Table 6 also presents the number of STAR elements in which each over-represented oligonucleotide is found. For example, the most significant oligonucleotide, oligo 1 (CCCCAC (SEQ ID NO:177)), occurs 107 times, but is found in only 51 STARs, i.e., on average it occurs as two copies per STAR. The least abundant oligonucleotide, number 166 (AATCGG (SEQ ID NO:342)), occurs on average as a single copy per STAR (thirteen occurrences on eleven STARs); single-copy oligonucleotides occur frequently, especially for the lower-abundance oligos. At the other extreme, oligo 4 (CAGCCC (SEQ ID NO:527)) occurs on average three times in those STARs in which it is found (37 STARs). The most widespread oligonucleotide is number 120 (CCCAGG (SEQ ID NO:296)), which occurs on 58 STARs (on average twice per STAR), and the least widespread oligonucleotide is number 114 (CGTCGC (SEQ ID NO:290)), which occurs on only six STARs (and on average only once per STAR).

Results of dyad frequency analysis are given in Table 7. Seven hundred thirty (730) dyads were found to be over-represented in the set of STAR elements (sig ≧0) compared to the reference sequence. The most significantly over-represented dyad, CCCN{2}CGG (SEQ ID NO:343), occurs 36 times among the 65 STAR elements, but is expected to occur only seven times. It has a significance coefficient of 9.31; in other words, the probability that its over-representation is due to chance is 1/10^9.31, i.e., less than one in two billion.

Three hundred ninety-seven (397) of the dyads have a significance coefficient greater than 1, and are, therefore, highly over-represented in the STAR elements. Among the over-represented dyads, their observed and expected occurrences, respectively, range from 9 and 1 (for five dyads (numbers 380, 435, 493, 640, and 665)) to 118 and 63 (for number 30 (AGGN{2}GGG (SEQ ID NO:372)), sig=4.44).

The oligonucleotides and dyads found to be over-represented in STAR elements by pattern frequency analysis were tested for their discriminative power by Linear Discriminant Analysis. Discriminant models were trained by step-wise selection of the best combination among the 50 most discriminant oligonucleotide (Table 6) or dyad (Table 7) patterns. The models achieved optimal error rates after incorporation of four (dyad) or five variables. The discriminative variables from oligo analysis are

numbers

11, 30, 94, 122, and 160 (Table 6); those from dyad analysis are numbers 73, 194, 419, and 497 (Table 7).

The discriminant models were then used to classify the 65 STAR elements in the training set and their associated random sequences. The model using oligonucleotide variables classifies 46 of the 65 STAR elements as STAR elements (true positives); the dyad model classifies 49 of the STAR elements as true positives. In combination, the models classify 59 of the 65 STAR elements as STAR elements (91%; FIG. 18). The false positive rates (random sequences classified as STARs) were seven for the dyad model, eight for the oligonucleotide model, and 13 for the combined predictions of the two models (20%). The STAR elements of Table 3 that were not classified as STARs by LDA are STAR7, STAR22, STAR35, STAR44, STAR46, and STAR65 (SEQ ID NOS:7, 22, 35, 44, 46 and 65, respectively). These elements display stabilizing anti-repressor activity in functional assays, so the fact that they are not classified as STARs by LDA suggests that they represent another class (or classes) of STAR elements.

The models were then used to classify the 19 candidate STAR elements in the testing set listed in Table 8. The dyad model classifies 12 of these candidate STARs as STAR elements, and the oligonucleotide model classifies 14 as STARs. The combined number of the candidates that are classified as STAR elements is 15 (79%). This is a lower rate of classification than obtained with the training set of 65 STARs; this is expected for two reasons. First, the discriminant models were trained with the 65 STARs of Table 3, and discriminative variables based on this training set may be less well represented in the testing set. Second, the candidate STAR sequences in the testing set have not yet been fully characterized in terms of in vivo function, and may include elements with only weak anti-repression properties.

This analysis demonstrates the power of a statistical approach to bio-informatic classification of STAR elements. The STAR sequences contain a number of dyad and hexameric oligonucleotide patterns that are significantly over-represented in comparison with the human genome as a whole. These patterns may represent binding sites for proteins that confer STAR activity; in any case they form a set of sequence motifs that can be used to recognize STAR element sequences.

Using these patterns to recognize STAR elements by Discriminant Analysis, a high proportion of the elements obtained by the genetic screen of the invention are in fact classified as STARs. This reflects underlying sequence and functional similarities among these elements. An important aspect of the method described here (pattern frequency analysis followed by Discriminant Analysis) is that it can be reiterated; for example, by including the 19 candidate STAR elements of Table 8 with the 66 STAR elements of Table 3 into one training set, an improved discriminant model can be trained. This improved model can then be used to classify other candidate regulatory elements as STARs. Large-scale in vivo screening of genomic sequences using the method of the invention, combined with reiteration of the bio-informatic analysis, will provide a means of discriminating STAR elements that asymptotically approaches 100% recognition and prediction of elements as the genome is screened in its entirety. These stringent and comprehensive predictions of STAR function will ensure that all human STAR elements are recognized, and are available for use in improving transgene expression.

Example 13 Cloning and Characterization of STAR Elements from Arabidopsis thaliana

Transgene silencing occurs in transgenic plants at both the transcriptional and post-transcriptional levels (Meyer, 2000, Vance and Vaucheret, 2001). In either case, the desired result of transgene expression can be compromised by silencing; the low expression and instability of the transgene results in poor expression of desirable traits (e.g., pest resistance) or low yields of recombinant proteins. It also results in poor predictability: the proportion of transgenic plants that express the transgene at biotechnologically useful levels is low, which necessitates laborious and expensive screening of transformed individuals for those with beneficial expression characteristics. This example describes the isolation of STAR elements from the genome of the dicot plant Arabidopsis thaliana for use in preventing transcriptional transgene silencing in transgenic plants. Arabidopsis was chosen for this example because it is a well-studied model organism: it has a compact genome, it is amenable to genetic and recombinant DNA manipulations, and its genome has been sequenced (Bevan et al., 2001, Initiative, 2000, Meinke et al., 1998).

Materials and Methods

Genomic DNA was isolated from Arabidopsis thaliana ecotype Columbia as described (Stam et al., 1998) and partially digested with MboI. The digested DNA was size-fractionated to 0.5-2 kilobase pairs by agarose gel electrophoresis and purification from the gel (QIAquick® Gel Extraction Kit, QIAGEN® 28706), followed by ligation into the pSelect vector (supra). Transfection into the U-2 OS/Tet-Off/LexA-HP1 cell line and selection for zeocin resistance at low doxycycline concentration was performed as described (supra). Plasmids were isolated from zeocin resistant colonies and re-transfected into the U-2 OS/Tet-Off/LexA-HP1 cell line.

Sequencing of Arabidopsis genomic DNA fragments that conferred zeocin resistance upon re-transfection was performed as described (supra). The DNA sequences were compared to the sequence of the Arabidopsis genome by BLAST analysis ((Altschul et al., 1990); URL http://www.ncbi.nlm.nih.gov/blast/Blast).

STAR activity was tested further by measuring mRNA levels for the hygromycin- and zeocin-resistance genes in recombinant host cells by reverse transcription PCR (RT-PCR). Cells of the U-2 OS/Tet-Off/lexA-HP1 cell line were transfected with pSelect plasmids containing Arabidopsis STAR elements, the Drosophila scs element, or containing no insert (supra). These were cultivated on hygromycin for two weeks at high doxycycline concentration, then the doxycycline concentration was lowered to 0.1 ng/ml to induce the lexA-HP1 repressor protein. After ten days, total RNA was isolated by the RNeasy® mini kit (QIAGEN® 74104) as described by the manufacturer. First-strand cDNA synthesis was carried out using the RevertAid™ First Strand cDNA Synthesis kit (MBI Fermentas 1622) using oligo(dT)18 primer as described by the manufacturer. An aliquot of the cDNA was used as the template in a PCR reaction using primers D58 (SEQ ID NO:145) and D80 (SEQ ID NO:148) (for the zeocin marker), and D70 (SEQ ID NO:146) and D71 (SEQ ID NO:147) (for the hygromycin marker), and Taq DNA polymerase (Promega M2661). The reaction conditions were 15-20 cycles of 94° C. for one minute, 54° C. for one minute, and 72° C. for 90 seconds. These conditions result in a linear relationship between input RNA and PCR product DNA. The PCR products were resolved by agarose gel electrophoresis, and the zeocin and hygromycin bands were detected by Southern blotting as described (Sambrook et al., 1989), using PCR products produced as above with purified pSelect plasmid as template. The ratio of the zeocin and hygromycin signals corresponds to the normalized expression level of the zeocin gene.

Results

The library of Arabidopsis genomic DNA in the pSelect vector comprised 69,000 primary clones in E. coli, 80% of which carried inserts. The average insert size was approximately 1000 base pairs; the library, therefore, represents approximately 40% of the Arabidopsis genome.

A portion of this library (representing approximately 16% of the Arabidopsis genome) was transfected into the U-2 OS/Tet-Off/LexA-HP1 cell line. Hygromycin selection was imposed to isolate transfectants, which resulted in 27,000 surviving colonies. These were then subjected to zeocin selection at low doxycycline concentration. Putative STAR-containing plasmids from 56 zeocin-resistant colonies were rescued into E. coli and re-transfected into U-2 OS/Tet-Off/LexA-HP1 cells. Forty-four of these plasmids (79% of the plasmids tested) conferred zeocin resistance on the host cells at low doxycycline concentrations, demonstrating that the plasmids carried STAR elements. This indicates that the pSelect screen in human U-2 OS cells is highly efficient at detection of STAR elements from plant genomic DNA.

The DNA sequences of these 44 candidate STAR elements were determined. Thirty-five of them were identified as single loci in the database of Arabidopsis nuclear genomic sequence (Table 9; SEQ ID NO:85-SEQ ID NO:119). Four others were identified as coming from the chloroplast genome, four were chimeras of DNA fragments from two loci, and one was not found in the Arabidopsis genome database.

The strength of the cloned Arabidopsis STAR elements was tested by assessing their ability to prevent transcriptional repression of the zeocin-resistance gene, using an RT-PCR assay. As a control for RNA input among the samples, the transcript levels of the hygromycin-resistance gene for each STAR transfection were assessed too. This analysis has been performed for 12 of the Arabidopsis STAR elements. The results (FIG. 19) demonstrate that the Arabidopsis STAR elements are superior to the Drosophila scs element (positive control) and the empty vector (“SV40”; negative control) in their ability to protect the zeocin-resistance gene from transcriptional repression. In particular, STAR-A28 (SEQ ID NO:112) and STAR-A30 (SEQ ID NO:114) enable two-fold higher levels of zeocin-resistance gene expression than the scs element (normalized to the internal control of hygromycin-resistance gene mRNA) when the lexA-HP1 repressor is expressed.

These results demonstrate that the method of the invention can be successfully applied to recovery of STAR elements from genomes of other species than human. Its successful application to STAR elements from a plant genome is particularly significant because it demonstrates the wide taxonomic range over which the method of the invention is applicable and because plants are an important target of biotechnological development.

Example 14 STAR Elements Function in CHO Cells

STAR elements function to block the effect of transcriptional repression influences on transgene expression units. Two of the benefits of STAR elements for heterologous protein production are an increased predictability to find high-expressing primary recombinant host cells as well as increased protein production or yield in these cells. Importantly, the disclosed STAR elements are human DNA sequences, isolated in the human U-2 OS osteosarcoma cell line. It is, therefore, an important question whether the human STAR elements are functional in a) cell lines derived from species other than man, and/or in b) human cell lines other than the U-2 OS osteosarcoma cell line. In this example the functionality of STAR 7 (SEQ ID NO:7) in (CHO) Chinese hamster ovary are illustrated.

Material and Methods

The STAR7 (SEQ ID NO:7) element is tested in the ppGIZ-STAR7 vector (FIG. 20). The construction of the pPlug&Play-GFP-ires-Zeo (ppGIZ) vector is described below. Plasmid pGFP (Clontech 6010-1) is modified by insertion of a linker at the BsiWI site to yield pGFP-link. The linker (made by annealing oligonucleotides 5′ GTACGGATATCAGATCTTTAATTAAG 3′ (SEQ ID NO:124) and 5′ GTACCTTAATTAAAGATCTGATATCC 3′ (SEQ ID NO:125)) introduces sites for the PacI, BglII, and EcoRV restriction endonucleases. This creates the multiple cloning site MCSII for insertion of STAR elements. Then primers 5′ ATCAGATCTGGCGCGCCATTTAAATCGTC TCGCGCGTTTCGGTGATGACGG 3′ (SEQ ID NO:126) and 5′ AGGCGGATCCGAATG TATTTAGAAAAATAAACAAATAGGGG 3′ (SEQ ID NO:127) are used to amplify a region of 0.37 kb from pGFP, which is inserted into the BglII site of pIRES (Clontech 6028-1) to yield pIRES-stuf. This introduces sites for the AscI and SwaI restriction endonucleases at MCSI, and acts as a “stuffer fragment” to avoid potential interference between STAR elements and adjacent promoters. pIRES-stuf is digested with BglII and FspI to liberate a DNA fragment composed of the stuffer fragment, the CMV promoter, the IRES element (flanked by multiple cloning sites MCS A and MCS B), and the SV40 polyadenylation signal. This fragment is ligated with the vector backbone of pGFP-link produced by digestion with BamHI and StuI, to yield pIRES-link.

The open reading frames of the zeocin-resistance gene is inserted into the BamHI/NotI sites of MCS B in pIRES-link as follows: the zeocin-resistance ORF is amplified by PCR with primers 5′ GATCGGATCCTTCGAAATGGCCAAGTTGACCAGTGC 3′ (SEQ ID NO:128) and 5′ AGGCGCGGCCGCAATTCTCAGTCCTGCTCCTC 3′ (SEQ ID NO:129) from plasmid pEM7/zeo, digested with BamHI and NotI, and ligated with BamHI/NotI-digested pIRES-link to yield pIRES-link-zeo. The GFP reporter ORF was introduced into pIRES-link-zeo by amplification of phr-GFP-1 with primers 5′ GATCGAATTCTCGCGAATGGTGAGCAAGCAGATCCTGAAG 3′ (SEQ ID NO:130) and 5′ AGGCGAATTCACCGGTGTTTAAACTTACACCCACTCGTGCAGGCTGCCCAGG 3′ (SEQ ID NO:131), and insertion of the EcoRI-digested GFP cassette into the EcoRI site in MCS A of the pIRES-link-zeo plasmid. This created the ppGIZ (for ppGFP-IRES-zeo). STAR7 (SEQ ID NO:7) is cloned into the SalI site (5′) and into the PacI site (3′).

Transfection and Culture of CHO Cells

The Chinese Hamster Ovary cell line CHO-K1 (ATCC CCL-61) is cultured in HAMS-F12 medium+10% Fetal Calf Serum containing 2 mM glutamine, 100 U/ml penicillin, and 100 micrograms/ml streptomycin at 37° C./5% CO₂. Cells are transfected with the plasmids using Lipofectamine 2000 (Invitrogen) as described by the manufacturer. Briefly, cells are seeded to culture vessels and grown overnight to 70-90% confluence. Lipofectamine reagent is combined with plasmid DNA at a ratio of 7.5 microliters per 3 microgram (e.g., for a 10 cm Petri dish, 20 micrograms DNA and 120 microliters Lipofectamine) and added after a 30-minute incubation at 25° C. to the cells. After a six-hour incubation, the transfection mixture is replaced with fresh medium, and the transfected cells are incubated further. After overnight cultivation, cells are trypsinized and seeded into fresh petri dishes with fresh medium with zeocin added to a concentration of 100 μg/ml and the cells are cultured further. When individual colonies become visible (approximately ten days after transfection) medium is removed and replaced with fresh medium without zeocin. Individual clones are isolated and transferred to 24-well plates in medium with zeocin. Expression of the GFP reporter gene is assessed approximately three weeks after transfection.

The tested constructs consist of a bicistronic gene with the GFP gene, an IRES and the Zeocin resistance gene under control of the CMV promoter, but either with or without STAR7 (SEQ ID NO:7) element to flank the entire construct (FIG. 20). The constructs are transfected to CHO-K1 cells. Stable colonies are expanded before the GFP signal is determined on a XL-MCL Beckman Coulter flow cytometer. The mean of the GFP signal is taken as measure for the level of GFP expression and this is plotted in FIG. 20.

Results

FIG. 20 shows that flanking a GFP reporter gene that is under the control of the CMV promoter results in a higher number of CHO colonies that express significantly higher levels of GFP protein, as compared to the control without STAR7 (SEQ ID NO:7) element. The STAR7 (SEQ ID NO:7) element, therefore, conveys a higher degree of predictability of transgene expression in CHO cells. The highest GFP expression level in STAR-shielded CHO colonies is also higher than in STAR-less control colonies. In addition, when the tested colonies were further grown for another 30 days without Zeocin in the culture medium, the GFP expression levels in the STAR-shielded colonies remained equally high, whereas the GFP expression levels in the STAR-less colonies dropped to at least below 50% of the original values. It is, therefore, concluded that STAR7 (SEQ ID NO:7) is able to convey higher as well as more stable expression levels to a transgene in CHO cells, this being a cell line derived from another species than man.

Example 15 STAR Elements Function in NSO Cells

STAR elements function to block the effect of transcriptional repression influences on transgene expression units. Two of the benefits of STAR elements for heterologous protein production are an increased predictability to find high-expressing primary recombinant host cells, as well as increased protein production or yield in these cells. Importantly, the disclosed STAR elements are human DNA sequences, isolated in the human U-2 OS osteosarcoma cell line. It is, therefore, an important question whether the human STAR elements are functional in a) cell lines derived from species other than man, and/or in b) human cell lines other than the U-2 OS osteosarcoma cell line. In this example the functionality of STAR 7 (SEQ ID NO:7) in non-secreting mouse myeloma (NSO) cells are illustrated.

Materials and Methods

The tested constructs are the same as described in Example 14. NSO (Non-Secreting mouse myeloma) cells (ECACC 85110503) are suspension cells that are cultured in RPMI 1640 medium+10% Fetal Calf Serum containing 2 mM glutamine, 100 U/ml penicillin, and 100 micrograms/ml streptomycin at 37° C./5% CO₂. Cells are transfected with the plasmids using Lipofectamine 2000 (Invitrogen) as described by the manufacturer. Briefly, cells are seeded to culture vessels and grown overnight to 4×10⁵/ml. Lipofectamine reagent is combined with plasmid DNA at a ratio of 3 microliters per microgram DNA (e.g., for a 10 cm Petri dish, 20 micrograms DNA and 60 microliters Lipofectamine) and added after 30 minutes incubation at 25° C. temperature to the cells. After overnight incubation, the transfection mixture is replaced with fresh medium and the transfected cells are incubated further. After another overnight incubation, zeocin is added to a concentration of 100 μg/ml and the cells are cultured and further incubated for three days. Then the cells are seeded in 96-well plates in such dilutions that one well will contain ˜1 cell. After ten days growing colonies are transferred to 24-well plates.

Results

FIG. 21 shows that flanking a GFP reporter gene that is under the control of the CMV promoter results in a higher number of NSO colonies that express significantly higher levels of GFP protein, as compared to the control without STAR7 (SEQ ID NO:7) element. The STAR7 (SEQ ID NO:7) element, therefore, conveys a higher degree of predictability of transgene expression in NSO cells. The highest GFP expression level in STAR-shielded NSO colonies is also higher than in STAR-less control colonies. It is, therefore, concluded that STAR7 (SEQ ID NO:7) is able to convey higher expression levels to a transgene in NSO cells, this being a cell line derived from another species than man.

Example 16 STAR Elements Function in Human 293 Cells

STAR elements function to block the effect of transcriptional repression influences on transgene expression units. Two of the benefits of STAR elements for heterologous protein production are an increased predictability to find high-expressing primary recombinant host cells as well as increased protein production or yield in these cells. Importantly, the disclosed STAR elements are human DNA sequences, isolated in the human U-2 OS osteosarcoma cell line. It is, therefore, an important question whether the human STAR elements are functional in a) cell lines derived from species other than man, and/or in b) human cell lines other than the U-2 OS osteosarcoma cell line. In this example, the functionality of STAR7 (SEQ ID NO:7) in human 293 cells are illustrated.

Materials and Methods

The tested constructs are the same as described in Example 14. The 293 cell line (ATCC CRL-1573) is derived from human embryonal kidney (immortalized by adenovirus 5 transfection) and is cultured in Dulbecco's Modified Eagle Medium+10% Fetal Calf Serum containing 2 mM glutamine, 100 U/ml penicillin, and 100 micrograms/ml streptomycin at 37° C./5% CO₂. Cells are transfected with the plasmids using Lipofectamine 2000 (Invitrogen) as described by the manufacturer. Selection and propagation of the 293 colonies are as described in Example 14 for U-2 OS cells.

Results

FIG. 22 shows that flanking a GFP reporter gene that is under the control of the CMV promoter results in a higher number of 293 colonies that express significantly higher levels of GFP protein, as compared to the control without STAR7 (SEQ ID NO:7) element. The STAR7 (SEQ ID NO:7) element, therefore, conveys a higher degree of predictability of transgene expression in 293 cells. The highest GFP expression level in STAR-shielded colonies is also higher than in STAR-less control colonies. It is, therefore, concluded that STAR7 (SEQ ID NO:7) is able to convey higher expression levels to a transgene in 293 cells, this being another human cell line, distinct from the human U-2 OS cell line.

TABLE 1

Biopharmaceutical Proteins, Their Tissue or Cell Type of Origin

Protein	Tissue/Somatic Cells	Cell Lines (ATCC #)¹	Indications

alpha-1 Antitrypsin	Liver, leukocytes	Hep G2 (HB-8065)	Cystic fibrosis, emphysema
alpha-Galactosidase A; -Glucosidase	Fibroblasts	WI 38 (CCL-75)	Fabry disease; Pompe's
			disease
Antibodies (monoclonal,	Lymphocytes	Transfectomas	Various therapeutic
single-chain, etc)			strategies
Antithrombin III	Liver	Hep G2 (HB-8065)	Thrombophilia
Calcitonin	Thyroid (parafollicular cells)	TT (CRL-1803)	Osteoporosis
Ciliary neurotrophic factor	Neural tissue (e.g., astrocytes)	HCN-1A (CRL-10442)	Motor neuron disease
Epidermal Growth Factor	Kidney	G-401 (CRL-1441)	Wound healing
Erythropoietin	Liver, kidney	Hep G2 (HB-8065),	Anemia
		G-401 (CRL-1441)
Factors VII, VIII, IX	Endothelial cells	HUV-EC-C (CRL-1730)	Hemophilia
Famoxin (recombinant gAcrp30)	Adipocytes	NA²	Obesity
Fibroblast growth factor (basic)	Cerebral cortex, hypothalamus	HCN-1A (CRL-10442)	Wound healing, angiogenesis
Gastric lipase	Pancreas	BxPC-3 (CRL-1687)	Pancreatic insufficiency,
			cystic fibrosis
Glucocerebrosidase	Macrophages	U-937 (CRL-1593.2)	Gaucher disease
Granulocyte macrophage-colony	T-lymphocytes	J.CaM1.6 (CRL-2063)	Chemotherapy neutropenia
stimulatin factor
Human growth hormone	Pituitary gland	HP75 (CRL-2506)	Growth retardation, Turner's
(somatotropin)			syndrome
Human serum albumin	Liver (hepatocytes)	Hep G2 (HB-8065)	Blood replacement (surgery,
			burns)
Insulin	Pancreas (Islet beta cells)	BxPC-3 (CRL-1687)	Diabetes
Interferons alpha	Leukocytes	WBC264-9C (HB-8902)	Cancer, hepatitis C
Interferons beta	Fibroblasts	WI 38 (CCL-75)	Multiple sclerosis
Interleukin-2, -4, -10	T-lymphocytes	J.CaM1.6 (CRL-2063)	Cancer, rheumatoid arthritis,
			hepatitis
Interleukin-18	Monocytes and macrophages	U-937 (CRL-1593.2)	Cancer, bacterial infections
Interleukin-1 Receptor Antagonist	Epithelium	HBE4-E6/E7 (CRL-2078)	Rheumatoid arthritis
Soluble Tumor Necrosis Factor	Placenta, spleen, fibroblasts	BeWo (CCL-98)	Rheumatoid arthritis,
receptor			multiple sclerosis
van Willebrand's factor	Endothelial cells	HUV-EC-C (CRL-1730)	Hemophilia

¹These cell lines are offered only as examples of cultured cells corresponding to the tissues and somatic cells; ATCC #: American Type Culture Collection accession number
²NA: Not Available; adipocytes can be differentiated from various other cell types

TABLE 2

Oligonucleotides used for polymerase chain
reactions (PCR primers) or DNA mutagenesis
(SEQ ID NOS:134-176)

SEQ ID NO:	Number	Sequence

134	C65	AACAAGCTTGATATCAGATCTGCTAGCTTGGT
		CGAGCTGATACTTCCC

135	C66	AAACTCGAGCGGCCGCGAATTCGTCGACTTTA
		CCACTCCCTATCAGTGATAGAG

136	C67	AAACCGCGGCATGGAAGACGCCAAAAACATAA
		AGAAAGG

137	C68	TATGGATCCTAGAATTACACGGCGATCTTTCC

138	C81	AAACCATGGCCGAGTACAAGCCCACGGTGCG
		CC

139	C82	AAATCTAGATCAGGCACCGGGCTTGCGGGTCA
		TGC

140	C85	CATTTCCCCGAAAAGTGCCACC

141	D30	TCACTGCTAGCGAGTGGTAAACTC

142	D41	GAAGTCGACGAGGCAGGCAGAAGTATGC

143	D42	GAGCCGCGGTTTAGTTCCTCACCTTGTCG

144	D51	TCTGGAAGCTTTGCTGAAGAAAC

145	D58	CCAAGTTGACCAGTGCC

146	D70	TACAAGCCAACCACGGCCT

147	D71	CGGAAGTGCTTGACATTGGG

148	D80	GTTCGTGGACACGACCTCCG

149	D89	GGGCAAGATGTCGTAGTCAGG

150	D90	AGGCCCATGGTCACCTCCATCGCTACTGTG

151	D91	CTAATCACTCACTGTGTAAT

152	D93	AATTACAGGCGCGCC

153	D94	AATTGGCGCGCCTGT

154	D95	TGCTTTGCATACTTCTGCCTGCCTC

155	E12	TAGGGGGGATCCAAATGTTC

156	E13	CCTAAAAGAAGATCTTTAGC

157	E14	AAGTGTTGGATCCACTTTGG

158	E15	TTTGAAGATCTACCAAATGG

159	E16	GTTCGGGATCCACCTGGCCG

160	E17	TAGGCAAGATCTTGGCCCTC

161	E18	CCTCTCTAGGGATCCGACCC

162	E19	CTAGAGAGATCTTCCAGTAT

163	E20	AGAGTTCCGGATCCGCCTGG

164	E21	CCAGGCAGACTCGGAACTCT

165	E22	TGGTGAAACCGGATCCCTAC

166	E23	AGGTCAGGAGATCTAGACCA

167	E25	CCATTTTCGCTTCCTTAGCTCC

168	E42	CGATGTAACCCACTCGTGCACC

169	E57	AGAGATCTAGGATAATTTCG

170	E92	AGGCGCTAGCACGCGTTCTACTCTTTTCCTAC
		TCTG

171	E93	GATCAAGCTTACGCGTCTAAAGGCATTTTATA
		TAG

172	E94	AGGCGCTAGCACGCGTTCAGAGTTAGTGATCC
		AGG

173	E95	GATCAAGCTTACGCGTCAGTAAAGGTTTCGTA
		TGG

174	E96	AGGCGCTAGCACGCGTTCTACTCTTTCATTAC
		TCTG

175	E97	CGAGGAAGCTGGAGAAGGAGAAGCTG

176	E98	CAAGGGCCGCAGCTTACACATGTTC

TABLE 3

STAR elements of the invention, including genomic location and
length (SEQ ID NOS: 1-66)

STAR	SEQ ID NO:	Location¹	Length

1	1	2q31.1	750
2	2	7p15.2	916
3	3	15q11.2 and 10q22.2	2132
4	4	1p31.1 and 14q24.1	1625
5	5	20q13.32	1571
6	6	2p21	1173
7	7	1q34	2101
8	8	9q32	1839
9	9	10p15.3	1936
10	10	Xp11.3	1167
11	11	2p25.1	1377
12	12	5q35.3	1051
13	13	9q34.3	1291
14	14	22q11.22	732
15	15	1p36.31	1881
16	16	1p21.2	1282
17	17	2q31.1	793
18	18	2q31.3	497
19	19	6p22.1	1840
20	20	8p13.3	780
21	21	6q24.2	620
22	22	2q12.2	1380
23	23	6p22.1	1246
24	24	1q21.2	948
25	25	1q21.3	1067
26	26	1q21.1	540
27	27	1q23.1	1520
28	28	22q11.23	961
29	29	2q13.31	2253
30	30	22q12.3	1851
31	31	9q34.11 and 22q11.21	1165
32	32	21q22.2	771
33	33	21q22.2	1368
34	34	9q34.14	755
35	35	7q22.3	1211
36	36	21q22.2	1712
37	37	22q11.23	1331
38	38	22q11.1 and 22q11.1	~1000
39	39	22q12.3	2331
40	40	22q11.21	1071
41	41	22q11.21	1144
42	42	22q11.1	735
43	43	14q24.3	1231
44	44	22q11.1	1591
45	45	22q11.21	1991
46	46	22q11.23	1871
47	47	22q11.21	1082
48	48	22q11.22	1242
49	49	Chr 12 random clone, and	1015
		3q26.32
50	50	6p21.31	2361
51	51	5q21.3	2289
52	52	7p15.2	1200
53	53	Xp11.3	1431
54	54	4q21.1	981
55	55	15q13.1	501
56	56	includes 3p25.3	741
57	57	4q35.2	1371
58	58	21q11.2	1401
59	59	17 random clone	872
60	60	4p16.1 and 6q27	2068
61	61	7p14.3 and 11q25	1482
62	62	14q24.3	1011
63	63	22q13.3	1421
64	64	17q11.2	1414
65	65	7q21.11 = 28.4	1310
66	66	20q13.33 and 6q14.1	~2800

¹Chromosomal location is determined by BLAST search of DNA sequence data from the STAR elements against the human genome database. The location is given according to standard nomenclature referring to the cytogenetic ideogram of each chromosome; e.g., 1p2.3 is the third cytogenetic sub-band of the second cytogenetic band of the short arm of chromosome 1 (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Genetics/chrombanding.html). F, forward sequencing reaction result; R, reverse sequencing reaction result.

TABLE 4

STAR elements convey stability over time on transgene
expression¹

	Cell Divisions²	Luciferase Expression³

STAR6 (SEQ ID NO: 6)	42	18,000
plus puromycin	60	23,000
	84	20,000
	108	16,000
STAR6 (SEQ ID NO: 6)	84	12,000
without puromycin⁴	108	15,000
	144	12,000

¹Plasmid pSDH-Tet-STAR6 was transfected into U-2 OS cells, and clones were isolated and cultivated in doxycycline-free medium as described in Example 1. Cells were transferred to fresh culture vessels weekly at a dilution of 1:20.
²The number of cell divisions is based on the estimation that in one week the culture reaches cell confluence, which represents ~6 cell divisions.
³Luciferase was assayed as described in Example 1.
⁴After 60 cell divisions the cells were transferred to two culture vessels; one was supplied with culture medium that contained puromycin, as for the first 60 cell divisions, and the second was supplied with culture medium lacking antibiotic.

TABLE 5

Human STAR elements and their putative mouse orthologs and
paralogs

NUMBER	STAR	Human¹	Mouse²	Similarity³	SEQ ID NO:

1	1	2q31.1	2D	600 bp 69%	1
2	2	7p15.2	6B3	909 bp 89%	2
3	3a	5q33.3	11B2	248 bp 83%	3
4	3b	10q22.2	14B	1. 363 bp 89%	3
				2. 163 bp 86%
5	6	2p21	17E4	437 bp 78%	6
6	12	5q35.3	11b1.3	796 bp 66%	12
7	13	9q34.3	2A3	753 bp 77%	13
8	18	2q31.3	2E1	497 bp 72%	18
9	36	21q22.2	16C4	166 bp 79%	36
10	40	22q11.1	6F1	1. 270 bp 75%	40
				2. 309 bp 70%
11	50	6p21.31	17B1	1. 451 bp 72%	50
				2. 188 bp 80%
				3. 142 bp 64%
12	52	7p15.2	6B3	1. 846 bp 74%	52
				2. 195 bp 71%
13	53	Xp11.3	XA2	364 bp 64%	53
14	54	4q21.1	5E3	1. 174 bp 80%	54
				2. 240 bp 73%
				3. 141 bp 67%
				4. 144 bp 68%
15	61a	7p14.3	6B3	188 bp 68%	61

¹Cytogenetic location of STAR element in the human genome.
²Cytogenetic location of STAR element ortholog in the mouse genome.
³Length of region(s) displaying high sequence similarity, and percentage similarity. In some cases more than one block of high similarity occurs; in those cases, each block is described separately. Similarity <60% is not considered significant.

The patterns are ranked according to significance coefficient. These were determined using RSA-Tools with the sequence of the human genome as reference. Patterns that comprise the most discriminant variables in Linear Discriminant Analysis are indicated with an asterisk. (SEQ ID NOS:177-342)

TABLE 6

Oligonucleotide patterns (6 base pairs) over-represented in
STAR elements.

					Number of
	Oligonucleotide	Observed	Expected	Significance	matching	SEQ ID
Number	sequence	occurrences	occurrences	coefficient	STARs	NO:

1	CCCCAC	107	49	8.76	51	177

2	CAGCGG	36	9	7.75	23	178

3	GGCCCC	74	31	7.21	34	179

4	CAGCCC	103	50	7.18	37	180

5	GCCCCC	70	29	6.97	34	181

6	CGGGGC	40	12	6.95	18	182

7	CCCCGC	43	13	6.79	22	183

8	CGGCAG	35	9	6.64	18	184

9	AGCCCC	83	38	6.54	40	185

10	CCAGGG	107	54	6.52	43	186

11	GGACCC *	58	23	6.04	35	187

12	GCGGAC	20	3	5.94	14	188

13	CCAGCG	34	10	5.9	24	189

14	GCAGCC	92	45	5.84	43	190

15	CCGGCA	28	7	5.61	16	191

16	AGCGGC	27	7	5.45	17	192

17	CAGGGG	86	43	5.09	43	193

18	CCGCCC	43	15	5.02	18	194

19	CCCCCG	35	11	4.91	20	195

20	GCCGCC	34	10	4.88	18	196

21	GCCGGC	22	5	4.7	16	197

22	CGGACC	19	4	4.68	14	198

23	CGCCCC	35	11	4.64	19	199

24	CGCCAG	28	8	4.31	19	200

25	CGCAGC	29	8	4.29	20	201

26	CAGCCG	32	10	4	24	202

27	CCCACG	33	11	3.97	26	203

28	GCTGCC	78	40	3.9	43	204

29	CCCTCC	106	60	3.87	48	205

30	CCCTGC *	92	50	3.83	42	206

31	CACCCC	77	40	3.75	40	207

32	GCGCCA	30	10	3.58	23	208

33	AGGGGC	70	35	3.55	34	209

34	GAGGGC	66	32	3.5	40	210

35	GCGAAC	14	2	3.37	13	211

36	CCGGCG	17	4	3.33	12	212

37	AGCCGG	34	12	3.29	25	213

38	GGAGCC	67	34	3.27	40	214

39	CCCCAG	103	60	3.23	51	215

40	CCGCTC	24	7	3.19	19	216

41	CCCCTC	81	44	3.19	43	217

42	CACCGC	33	12	3.14	22	218

43	CTGCCC	96	55	3.01	42	219

44	GGGCCA	68	35	2.99	39	220

45	CGCTGC	28	9	2.88	22	221

46	CAGCGC	25	8	2.77	19	222

47	CGGCCC	28	10	2.73	19	223

48	CCGCCG	19	5	2.56	9	224

49	CCCCGG	30	11	2.41	17	225

50	AGCCGC	23	7	2.34	17	226

51	GCACCC	55	27	2.31	38	227

52	AGGACC	54	27	2.22	33	228

53	AGGGCG	24	8	2.2	18	229

54	CAGGGC	81	47	2.18	42	230

55	CCCGCC	45	21	2.15	20	231

56	GCCAGC	66	36	2.09	39	232

57	AGCGCC	21	6	2.09	18	233

58	AGGCCC	64	34	2.08	32	234

59	CCCACC	101	62	2.05	54	235

60	CGCTCA	21	6	2.03	17	236

61	AACGCG	9	1	1.96	9	237

62	GCGGCA	21	7	1.92	14	238

63	AGGTCC	49	24	1.87	36	239

64	CCGTCA	19	6	1.78	14	240

65	CAGAGG	107	68	1.77	47	241

66	CCCGAG	33	14	1.77	22	242

67	CCGAGG	36	16	1.76	25	243

68	CGCGGA	11	2	1.75	8	244

69	CCACCC	87	53	1.71	45	245

70	CCTCGC	23	8	1.71	20	246

71	CAAGCC	59	32	1.69	40	247

72	TCCGCA	18	5	1.68	17	248

73	CGCCGC	18	5	1.67	9	249

74	GGGAAC	55	29	1.63	39	250

75	CCAGAG	93	58	1.57	49	251

76	CGTTCC	19	6	1.53	16	252

77	CGAGGA	23	8	1.5	19	253

78	GGGACC	48	24	1.48	31	254

79	CCGCGA	10	2	1.48	8	255

80	CCTGCG	24	9	1.45	17	256

81	CTGCGC	23	8	1.32	14	257

82	GACCCC	47	24	1.31	33	258

83	GCTCCA	66	38	1.25	39	259

84	CGCCAC	33	15	1.19	21	260

85	GCGGGA	23	9	1.17	18	261

86	CTGCGA	18	6	1.15	15	262

87	CTGCTC	80	49	1.14	50	263

88	CAGACG	23	9	1.13	19	264

89	CGAGAG	21	8	1.09	17	265

90	CGGTGC	18	6	1.06	16	266

91	CTCCCC	84	53	1.05	47	267

92	GCGGCC	22	8	1.04	14	268

93	CGGCGC	14	4	1.04	13	269

94	AAGCCC *	60	34	1.03	42	270

95	CCGCAG	24	9	1.03	17	271

96	GCCCAC	59	34	0.95	35	272

97	CACCCA	92	60	0.93	49	273

98	GCGCCC	27	11	0.93	18	274

99	ACCGGC	15	4	0.92	13	275

100	CTCGCA	16	5	0.89	14	276

101	ACGCTC	16	5	0.88	12	277

102	CTGGAC	58	33	0.88	32	278

103	GCCCCA	67	40	0.87	38	279

104	ACCGTC	15	4	0.86	11	280

105	CCCTCG	21	8	0.8	18	281

106	AGCCCG	22	8	0.79	14	282

107	ACCCGA	16	5	0.78	13	283

108	AGCAGC	79	50	0.75	41	284

109	ACCGCG	14	4	0.69	7	285

110	CGAGGC	29	13	0.69	24	286

111	AGCTGC	70	43	0.64	36	287

112	GGGGAC	49	27	0.64	34	288

113	CCGCAA	16	5	0.64	12	289

114	CGTCGC	8	1	0.62	6	290

115	CGTGAC	17	6	0.57	15	291

116	CGCCCA	33	16	0.56	22	292

117	CTCTGC	97	65	0.54	47	293

118	AGCGGG	21	8	0.52	17	294

119	ACCGCT	15	5	0.5	11	295

120	CCCAGG	133	95	0.49	58	296

121	CCCTCA	71	45	0.49	39	297

122	CCCCCA *	77	49	0.49	42	298

123	GGCGAA	16	5	0.48	14	299

124	CGGCTC	29	13	0.47	19	300

125	CTCGCC	20	8	0.46	17	301

126	CGGAGA	20	8	0.45	14	302

127	TCCCCA	95	64	0.43	52	303

128	GACACC	44	24	0.42	33	304

129	CTCCGA	17	6	0.42	13	305

130	CTCGTC	17	6	0.42	14	306

131	CGACCA	13	4	0.39	11	307

132	ATGACG	17	6	0.37	12	308

133	CCATCG	17	6	0.37	13	309

134	AGGGGA	78	51	0.36	44	310

135	GCTGCA	77	50	0.35	43	311

136	ACCCCA	76	49	0.33	40	312

137	CGGAGC	21	9	0.33	16	313

138	CCTCCG	28	13	0.32	19	314

139	CGGGAC	16	6	0.3	10	315

140	CCTGGA	88	59	0.3	45	316

141	AGGCGA	18	7	0.29	17	317

142	ACCCCT	54	32	0.28	36	318

143	GCTCCC	56	34	0.27	36	319

144	CGTCAC	16	6	0.27	15	320

145	AGCGCA	16	6	0.26	11	321

146	GAAGCC	62	38	0.25	39	322

147	GAGGCC	79	52	0.22	42	323

148	ACCCTC	54	32	0.22	33	324

149	CCCGGC	37	20	0.21	21	325

150	CGAGAA	20	8	0.2	17	326

151	CCACCG	29	14	0.18	20	327

152	ACTTCG	16	6	0.17	14	328

153	GATGAC	48	28	0.17	35	329

154	ACGAGG	23	10	0.16	18	330

155	CCGGAG	20	8	0.15	18	331

156	ACCCAC	60	37	0.12	41	332

157	CTGGGC	105	74	0.11	50	333

158	CCACGG	23	10	0.09	19	334

159	CGGTCC	13	4	0.09	12	335

160	AGCACC *	54	33	0.09	40	336

161	ACACCC	53	32	0.08	38	337

162	AGGGCC	54	33	0.08	30	338

163	CGCGAA	6	1	0.02	6	339

164	GAGCCC	58	36	0.02	36	340

165	CTGAGC	71	46	0.02	45	341

166	AATCGG	13	4	0.02	11	342

The patterns are ranked according to significance coefficient. These were determined using RSA-Tools with the random sequence from the human genome as reference. Patterns that comprise the most discriminant variables in Linear Discriminant Analysis are indicated with an asterisk. (SEQ ID NOS:343-1072)

TABLE 7

Dyad patterns over-represented in STAR elements.

		Observed	Expected	Significance	SEQ ID
Number	Dyad sequence	occurrences	occurrences	coefficient	NO:

1	CCCN{2}CGG	36	7	9.31	343

2	CCGN{6}CCC	40	10	7.3	344

3	CAGN{0}CGG	36	8	7.13	345

4	CGCN{15}CCC	34	8	6.88	346

5	CGGN{9}GCC	33	7	6.82	347

6	CCCN{9}CGC	35	8	6.72	348

7	CCCN{1}GCG	34	8	6.64	349

8	CCCN{0}CAC	103	48	6.61	350

9	AGCN{16}CCG	29	6	5.96	351

10	CCCN{4}CGC	34	8	5.8	352

11	CGCN{13}GGA	26	5	5.77	353

12	GCGN{16}CCC	30	7	5.74	354

13	CGCN{5}GCA	25	5	5.49	355

14	CCCN{14}CCC	101	49	5.43	356

15	CTGN{4}CGC	34	9	5.41	357

16	CCAN{12}GCG	28	6	5.37	358

17	CGGN{11}CAG	36	10	5.25	359

18	CCCN{5}GCC	75	33	4.87	360

19	GCCN{0}CCC	64	26	4.81	361

20	CGCN{4}GAC	19	3	4.78	362

21	CGGN{0}CAG	33	9	4.76	363

22	CCCN{3}CGC	32	8	4.67	364

23	CGCN{1}GAC	20	3	4.58	365

24	GCGN{2}GCC	29	7	4.54	366

25	CCCN{4}GCC	76	34	4.53	367

26	CCCN{1}CCC	103	52	4.53	368

27	CCGN{13}CAG	33	9	4.5	369

28	GCCN{4}GGA	64	27	4.48	370

29	CCGN{3}GGA	26	6	4.46	371

30	AGGN{2}GGG	118	63	4.44	372

31	CACN{5}GCG	22	4	4.42	373

32	CGCN{17}CCA	27	6	4.39	374

33	CCCN{9}GGC	69	30	4.38	375

34	CCTN{5}GCG	28	7	4.37	376

35	GCGN{0}GAC	19	3	4.32	377

36	GCCN{0}GGC	40	7	4.28	378

37	GCGN{2}CCC	26	6	4.27	379

38	CCGN{11}CCC	32	9	4.17	380

39	CCCN{8}TCG	23	5	4.12	381

40	CCGN{17}GCC	30	8	4.12	382

41	GGGN{5}GGA	101	52	4.11	383

42	GGCN{6}GGA	71	32	4.1	384

43	CCAN{4}CCC	96	48	4.1	385

44	CCTN{14}CCG	32	9	4.09	386

45	GACN{12}GGC	45	16	4.07	387

46	CGCN{13}CCC	30	8	4.04	388

47	CAGN{16}CCC	92	46	4.02	389

48	AGCN{10}GGG	75	35	3.94	390

49	CGGN{13}GGC	30	8	3.93	391

50	CGGN{1}GCC	30	8	3.92	392

51	AGCN{0}GGC	26	6	3.9	393

52	CCCN{16}GGC	64	28	3.89	394

53	GCTN{19}CCC	67	29	3.87	395

54	CCCN{16}GGG	88	31	3.81	396

55	CCCN{9}CGG	30	8	3.77	397

56	CCCN{10}CGG	30	8	3.76	398

57	CCAN{0}GCG	32	9	3.75	399

58	GCCN{17}CGC	26	6	3.74	400

59	CCTN{6}CGC	27	7	3.73	401

60	GGAN{1}CCC	63	27	3.71	402

61	CGCN{18}CAC	24	5	3.7	403

62	CGCN{20}CCG	21	4	3.69	404

63	CCGN{0}GCA	26	6	3.69	405

64	CGCN{20}CCC	28	7	3.69	406

65	AGCN{15}CCC	67	30	3.65	407

66	CCTN{7}GGC	69	31	3.63	408

67	GCCN{5}CGC	32	9	3.61	409

68	GCCN{14}CGC	28	7	3.59	410

69	CAGN{11}CCC	89	45	3.58	411

70	GGGN{16}GAC	53	21	3.57	412

71	CCCN{15}GCG	25	6	3.57	413

72	CCCN{0}CGC	37	12	3.54	414

73	CCCN{16}AGC *	67	30	3.54	415

74	AGGN{9}GGG	96	50	3.52	416

75	CGCN{12}CTC	28	7	3.46	417

76	CACN{8}CGC	23	5	3.43	418

77	CCAN{7}CCG	31	9	3.42	419

78	CGGN{1}GCA	25	6	3.41	420

79	CGCN{14}CCC	29	8	3.4	421

80	AGCN{0}CCC	76	36	3.4	422

81	CGCN{13}GTC	18	3	3.37	423

82	GCGN{3}GCA	26	7	3.35	424

83	CGGN{0}GGC	34	11	3.35	425

84	GCCN{14}CCC	68	31	3.33	426

85	ACCN{7}CGC	21	4	3.32	427

86	AGGN{7}CGG	33	10	3.31	428

87	CCCN{16}CGA	22	5	3.3	429

88	CGCN{6}CAG	31	9	3.29	430

89	CAGN{11}GCG	29	8	3.29	431

90	CCGN{12}CCG	19	4	3.26	432

91	CGCN{18}CAG	27	7	3.24	433

92	CAGN{1}GGG	80	39	3.21	434

93	CGCN{0}CCC	32	10	3.2	435

94	GCGN{18}GCC	26	7	3.18	436

95	CGGN{15}GGC	27	7	3.15	437

96	CCCN{15}AGG	72	34	3.14	438

97	AGGN{20}GCG	26	7	3.14	439

98	CGGN{5}CTC	26	7	3.13	440

99	TCCN{17}CGA	23	5	3.12	441

100	GCGN{4}CCC	30	9	3.08	442

101	CCCN{2}CGC	30	9	3.07	443

102	CGTN{3}CAG	28	8	3.06	444

103	CCGN{13}GAG	27	7	3.05	445

104	CTCN{6}CGC	28	8	3.04	446

105	CGCN{4}GAG	21	5	3.03	447

106	GCGN{5}GGA	24	6	3.03	448

107	CCGN{1}CAG	27	7	3.01	449

108	CGCN{11}CCG	18	3	2.99	450

109	GCGN{19}CCC	26	7	2.98	451

110	CGCN{18}GAA	21	5	2.98	452

111	GGGN{19}GGA	78	39	2.95	453

112	CCAN{1}CGG	24	6	2.94	454

113	CCCN{7}GCG	25	6	2.94	455

114	AGGN{10}CCC	84	43	2.92	456

115	CCAN{0}GGG	97	52	2.88	457

116	CAGN{10}CCC	82	41	2.87	458

117	CCGN{18}CCG	19	4	2.86	459

118	CCGN{18}GGC	26	7	2.85	460

119	CCCN{2}GCG	24	6	2.84	461

120	CGCN{1}GGC	25	7	2.83	462

121	CCGN{5}GAC	19	4	2.81	463

122	GGAN{0}CCC	52	22	2.8	464

123	CCCN{1}CCG	29	9	2.78	465

124	CCCN{15}ACG	23	6	2.75	466

125	AGCN{8}CCC	66	31	2.73	467

126	CCCN{3}GGC	60	27	2.71	468

127	AGGN{9}CGG	31	10	2.7	469

128	CCCN{14}CGC	27	8	2.7	470

129	CCGN{0}CCG	19	4	2.7	471

130	CGCN{8}AGC	23	6	2.69	472

131	CGCN{19}ACC	21	5	2.68	473

132	GCGN{17}GAC	17	3	2.66	474

133	AGCN{1}GCG	24	6	2.63	475

134	CCGN{11}GGC	31	10	2.63	476

135	CGGN{4}AGA	26	7	2.63	477

136	CGCN{14}CCG	17	3	2.62	478

137	CCTN{20}GCG	24	6	2.62	479

138	CCAN{10}CGC	26	7	2.61	480

139	CCCN{20}CAC	69	33	2.6	481

140	CCGN{11}GCC	27	8	2.6	482

141	CGCN{18}CCC	26	7	2.59	483

142	CGGN{15}CGC	16	3	2.57	484

143	CGCN{16}GCC	24	6	2.55	485

144	CGCN{20}GGC	23	6	2.54	486

145	CGCN{19}CCG	18	4	2.52	487

146	CGGN{10}CCA	28	8	2.51	488

147	CGCN{17}CCC	26	7	2.51	489

148	CGCN{11}ACA	23	6	2.51	490

149	CGGN{0}ACC	17	3	2.5	491

150	GCGN{10}GCC	24	6	2.49	492

151	GCGN{8}GAC	17	3	2.49	493

152	CCCN{15}GGG	84	32	2.44	494

153	CGGN{16}GGC	27	8	2.44	495

154	CGCN{16}CCA	23	6	2.42	496

155	GCCN{3}CCC	73	36	2.4	497

156	CAGN{4}GGG	94	51	2.4	498

157	CCCN{6}GCG	23	6	2.38	499

158	CCGN{16}CGC	17	3	2.38	500

159	CCCN{17}GCA	61	28	2.37	501

160	CGCN{13}TCC	24	6	2.37	502

161	GCCN{1}CGC	29	9	2.36	503

162	CCGN{19}GAG	26	7	2.35	504

163	GGGN{10}GGA	89	48	2.35	505

164	CAGN{5}CCG	32	11	2.35	506

165	CGCN{3}AGA	19	4	2.32	507

166	GCCN{0}GCC	29	9	2.32	508

167	CCCN{8}GGC	61	28	2.31	509

168	CCTN{6}GCG	22	6	2.29	510

169	GACN{6}CCC	48	20	2.29	511

170	CGGN{1}CCC	26	8	2.27	512

171	CCCN{15}CCG	30	10	2.27	513

172	CAGN{9}CCC	84	44	2.26	514

173	CGGN{10}GGC	27	8	2.26	515

174	CGAN{10}ACG	10	1	2.26	516

175	GCGN{3}TCC	21	5	2.26	517

176	CCCN{3}GCC	75	38	2.24	518

177	GCGN{1}ACC	17	3	2.24	519

178	CCGN{9}AGG	27	8	2.23	520

179	CGCN{16}CAG	26	8	2.23	521

180	GGCN{0}CCC	62	29	2.22	522

181	AGGN{12}CCG	26	8	2.19	523

182	CCGN{0}GCG	16	3	2.19	524

183	CCGN{2}GCC	30	10	2.18	525

184	CCGN{11}GTC	19	4	2.17	526

185	CAGN{0}CCC	88	47	2.17	527

186	CCCN{5}CCG	32	11	2.17	528

187	GCCN{20}CCC	66	32	2.15	529

188	GACN{2}CGC	18	4	2.14	530

189	CGCN{6}CAC	23	6	2.13	531

190	AGGN{14}GCG	25	7	2.1	532

191	GACN{5}CGC	17	3	2.1	533

192	CCTN{19}CCG	29	9	2.1	534

193	CCGN{12}GGA	24	7	2.08	535

194	GGCN{9}GAC *	44	18	2.08	536

195	AGGN{10}GGG	94	52	2.07	537

196	CCGN{10}GAG	25	7	2.07	538

197	CGCN{6}GGA	20	5	2.06	539

198	CGCN{7}AGC	23	6	2.04	540

199	CCAN{13}CGG	26	8	2.03	541

200	CGGN{6}GGA	25	7	2.03	542

201	CGCN{19}GCC	24	7	2.03	543

202	CCAN{12}CGC	24	7	2.02	544

203	CGGN{1}GGC	41	16	2.02	545

204	GCGN{3}CCA	25	7	2.01	546

205	AGGN{1}CGC	21	5	2	547

206	CTCN{5}CGC	24	7	1.98	548

207	CCCN{0}ACG	30	10	1.97	549

208	CAGN{17}CCG	29	9	1.96	550

209	GGCN{4}CCC	62	30	1.96	551

210	AGGN{8}GCG	26	8	1.96	552

211	CTGN{1}CCC	88	48	1.94	553

212	CCCN{16}CAG	85	46	1.94	554

213	CGCN{9}GAC	16	3	1.93	555

214	CAGN{6}CCG	29	9	1.92	556

215	CGTN{12}CGC	11	1	1.92	557

216	CTCN{7}GCC	69	35	1.92	558

217	CGCN{19}TCC	22	6	1.92	559

218	CCCN{7}GCC	67	33	1.91	560

219	CAGN{13}CGG	30	10	1.9	561

220	CGCN{1}GCC	27	8	1.9	562

221	CGCN{17}CCG	17	4	1.89	563

222	AGGN{4}CCC	63	31	1.89	564

223	AGCN{10}CGC	21	5	1.89	565

224	CCCN{11}CGG	30	10	1.88	566

225	CCCN{8}GCC	75	39	1.86	567

226	CCGN{1}CGG	22	3	1.86	568

227	CCCN{1}ACC	71	36	1.85	569

228	CGCN{0}CAG	25	7	1.85	570

229	CCGN{19}TGC	23	6	1.82	571

230	GCGN{4}CGA	12	2	1.82	572

231	CCGN{19}GCC	30	10	1.82	573

232	CCAN{10}CCC	85	46	1.81	574

233	CAGN{13}GGG	91	51	1.81	575

234	AGCN{18}CGG	23	6	1.81	576

235	CGAN{8}CGC	11	1	1.81	577

236	AGCN{4}CCC	63	31	1.8	578

237	GGAN{6}CCC	61	30	1.8	579

238	CGGN{13}AAG	23	6	1.8	580

239	ACCN{11}CGC	19	5	1.79	581

240	CCGN{12}CAG	28	9	1.78	582

241	CCCN{12}GGG	76	29	1.77	583

242	CACN{17}ACG	22	6	1.76	584

243	CAGN{18}CCC	82	44	1.76	585

244	CGTN{10}GTC	19	5	1.75	586

245	CCCN{13}GCG	23	6	1.75	587

246	GCAN{1}CGC	20	5	1.73	588

247	AGAN{4}CCG	24	7	1.73	589

248	GCGN{10}AGC	22	6	1.72	590

249	CGCN{0}GGA	12	2	1.72	591

250	CGGN{4}GAC	17	4	1.69	592

251	CCCN{12}CGC	26	8	1.68	593

252	GCCN{15}CCC	65	33	1.68	594

253	GCGN{6}TCC	20	5	1.66	595

254	CGGN{3}CAG	33	12	1.65	596

255	CCCN{3}CCA	88	49	1.65	597

256	AGCN{3}CCC	59	28	1.65	598

257	GGGN{16}GCA	65	33	1.65	599

258	AGGN{8}CCG	28	9	1.64	600

259	CCCN{0}CCG	29	10	1.64	601

260	GCGN{5}GAC	16	3	1.64	602

261	CCCN{9}ACC	60	29	1.64	603

262	CTGN{5}CGC	25	8	1.64	604

263	CGCN{14}CTC	23	7	1.64	605

264	CGGN{14}GCA	23	7	1.63	606

265	CCGN{8}GCC	26	8	1.62	607

266	CCGN{7}CAC	23	7	1.62	608

267	AGCN{8}GCG	21	6	1.61	609

268	CGGN{16}GGA	29	10	1.61	610

269	CCAN{12}CCG	26	8	1.61	611

270	CGGN{2}CCC	26	8	1.6	612

271	CCAN{13}GGG	71	37	1.6	613

272	CGGN{15}GCA	21	6	1.6	614

273	CGCN{9}GCA	20	5	1.58	615

274	CGGN{19}CCA	26	8	1.58	616

275	GGGN{15}CGA	20	5	1.57	617

276	CCCN{10}CGC	26	8	1.57	618

277	CTCN{14}CGC	26	8	1.55	619

278	CACN{11}GCG	20	5	1.55	620

279	CCGN{2}GGC	24	7	1.55	621

280	CTGN{18}CCC	85	47	1.54	622

281	GGGN{13}CAC	58	28	1.54	623

282	CCTN{15}GGC	62	31	1.54	624

283	CCCN{20}CGA	20	5	1.54	625

284	CCCN{8}CGA	20	5	1.53	626

285	GAGN{7}CCC	61	30	1.53	627

286	CGCN{2}CCG	22	6	1.53	628

287	CCCN{0}TCC	98	57	1.52	629

288	AGCN{0}GCC	21	6	1.52	630

289	CCCN{2}TCC	82	45	1.52	631

290	CCGN{5}CCC	30	10	1.52	632

291	CGCN{13}CGC	16	3	1.51	633

292	CCCN{1}CGC	28	9	1.51	634

293	GCCN{16}GCA	53	25	1.51	635

294	CCCN{16}CCA	84	46	1.5	636

295	CCGN{13}CGC	19	5	1.5	637

296	CCGN{17}CAG	28	9	1.49	638

297	CGGN{18}GGC	26	8	1.49	639

298	CCGN{14}AGG	23	7	1.49	640

299	CCCN{5}CGG	26	8	1.49	641

300	CCCN{6}GGA	58	28	1.49	642

301	ACGN{2}CCC	20	5	1.49	643

302	CCAN{9}CCG	27	9	1.48	644

303	CCCN{19}CCA	78	42	1.48	645

304	CAGN{0}GGG	77	41	1.48	646

305	AGCN{1}CCC	58	28	1.47	647

306	GCGN{7}TCC	27	9	1.46	648

307	ACGN{18}CCA	25	8	1.46	649

308	GCTN{14}CCC	61	30	1.46	650

309	GCGN{14}CCC	23	7	1.46	651

310	GCGN{19}AGC	20	5	1.45	652

311	CCGN{8}CAG	29	10	1.45	653

312	GCGN{6}GCC	22	6	1.45	654

313	GCGN{10}GCA	20	5	1.44	655

314	CCTN{7}GCC	69	36	1.44	656

315	GCCN{13}GCC	54	26	1.42	657

316	CCCN{14}GCC	63	32	1.42	658

317	CCCN{15}CGG	26	8	1.42	659

318	CCAN{13}CGC	23	7	1.42	660

319	AGCN{11}GGG	67	35	1.41	661

320	GGAN{0}GCC	64	32	1.4	662

321	GCCN{3}TCC	61	30	1.4	663

322	CCTN{5}GCC	69	36	1.39	664

323	CGGN{18}CCC	25	8	1.39	665

324	CCTN{3}GGC	59	29	1.38	666

325	CCGN{0}CTC	22	6	1.38	667

326	AGCN{17}GCG	19	5	1.37	668

327	ACGN{14}GGG	20	5	1.37	669

328	CGAN{12}GGC	19	5	1.37	670

329	CCCN{20}CGC	24	7	1.37	671

330	ACGN{12}CTG	24	7	1.36	672

331	CCGN{0}CCC	36	14	1.36	673

332	CCGN{10}GGA	23	7	1.36	674

333	CCCN{3}GCG	21	6	1.36	675

334	GCGN{14}CGC	22	3	1.35	676

335	CCGN{8}CGC	16	4	1.35	677

336	CGCN{10}ACA	22	6	1.34	678

337	CCCN{19}CCG	28	10	1.33	679

338	CACN{14}CGC	20	5	1.32	680

339	GACN{3}GGC	46	21	1.32	681

340	GAAN{7}CGC	19	5	1.32	682

341	CGCN{16}GGC	21	6	1.31	683

342	GGCN{9}CCC	64	33	1.31	684

343	CCCN{9}GCC	64	33	1.31	685

344	CGCN{0}TGC	26	9	1.3	686

345	CCTN{8}GGC	67	35	1.3	687

346	CCAN{8}CCC	82	46	1.29	688

347	GACN{2}CCC	42	18	1.28	689

348	GGCN{1}CCC	54	26	1.27	690

349	CGCN{0}AGC	24	7	1.26	691

350	AGGN{4}GCG	28	10	1.26	692

351	CGGN{6}TCC	22	6	1.25	693

352	ACGN{19}GGC	20	5	1.25	694

353	CCCN{8}ACG	21	6	1.24	695

354	CCCN{18}GCC	62	31	1.24	696

355	GCCN{2}CGA	19	5	1.24	697

356	CCCN{8}GCG	28	10	1.23	698

357	CCCN{0}CTC	76	41	1.23	699

358	GCCN{11}CGC	27	9	1.22	700

359	AGCN{9}CCC	59	29	1.22	701

360	GCTN{0}GCC	71	38	1.21	702

361	CGCN{3}CCC	26	9	1.21	703

362	CCCN{2}CCC	117	72	1.19	704

363	GCCN{9}CGC	23	7	1.19	705

364	GCAN{19}CGC	19	5	1.19	706

365	CAGN{4}CGG	32	12	1.18	707

366	CAGN{2}GGG	80	44	1.17	708

367	GCCN{16}CCC	67	35	1.16	709

368	GAGN{5}CCC	60	30	1.16	710

369	CCTN{16}TCG	20	6	1.16	711

370	CCCN{2}GGC	62	32	1.15	712

371	GCGN{13}GGA	24	8	1.15	713

372	GCCN{17}GGC	66	25	1.15	714

373	CCCN{14}GGC	58	29	1.14	715

374	AGGN{3}CCG	31	12	1.14	716

375	CACN{0}CGC	32	12	1.14	717

376	CGGN{18}CAG	28	10	1.14	718

377	AGCN{1}GCC	57	28	1.13	719

378	CGCN{18}GGC	23	7	1.13	720

379	CCCN{5}AGG	64	33	1.11	721

380	AACN{0}GCG	9	1	1.11	722

381	CCCN{10}CCA	88	50	1.09	723

382	CGCN{13}GAG	20	6	1.09	724

383	CGCN{7}GCC	25	8	1.08	725

384	CCCN{9}CCG	28	10	1.07	726

385	CGCN{16}CCC	24	8	1.05	727

386	GAAN{13}CGC	18	5	1.05	728

387	GGCN{3}CCC	49	23	1.03	729

388	TCCN{11}CCA	87	50	1.03	730

389	CACN{0}CCC	70	38	1.02	731

390	CGCN{16}CCG	15	3	1.02	732

391	CGGN{15}AGC	21	6	1.02	733

392	CCCN{12}GCG	21	6	1.02	734

393	CCCN{9}GAG	59	30	1.01	735

394	CCGN{20}TCC	24	8	1.01	736

395	CGCN{0}CGC	17	4	1.01	737

396	ATGN{7}CGG	20	6	1	738

397	GGGN{20}GCA	59	30	1	739

398	CGGN{4}GGC	26	9	0.99	740

399	CGGN{16}AGC	22	7	0.99	741

400	CGGN{5}GGC	25	8	0.99	742

401	GCGN{0}GGA	25	8	0.98	743

402	GGCN{20}CAC	52	25	0.98	744

403	CCCN{9}CCC	97	58	0.97	745

404	ACCN{17}GGC	44	20	0.97	746

405	CCCN{6}CGA	18	5	0.96	747

406	AAGN{10}CGG	26	9	0.96	748

407	CGCN{17}CAC	21	6	0.95	749

408	CCCN{16}CGG	25	8	0.94	750

409	GACN{18}GGC	39	17	0.94	751

410	GGGN{15}GAC	47	22	0.92	752

411	GCCN{4}TCC	66	35	0.92	753

412	GGCN{15}CCC	56	28	0.92	754

413	CAGN{12}CGC	24	8	0.92	755

414	CCAN{3}GCG	22	7	0.91	756

415	CCGN{16}GAG	22	7	0.9	757

416	AGCN{2}CGC	24	8	0.89	758

417	GAGN{4}CCC	54	27	0.89	759

418	AGGN{3}CGC	23	7	0.88	760

419	CACN{13}AGG *	67	36	0.88	761

420	CCCN{4}CAG	88	51	0.88	762

421	CCCN{2}GAA	63	33	0.87	763

422	CGCN{19}GAG	21	6	0.87	764

423	ACGN{18}GGG	21	6	0.87	765

424	CCCN{4}GGC	62	32	0.87	766

425	CGGN{9}GAG	28	10	0.86	767

426	CCCN{3}GGG	66	26	0.86	768

427	GAGN{4}GGC	66	35	0.85	769

428	CGCN{5}GAG	18	5	0.84	770

429	CCGN{20}AGG	24	8	0.84	771

430	CCCN{15}CCC	88	51	0.83	772

431	AGGN{17}CCG	25	8	0.82	773

432	AGGN{6}GGG	89	52	0.82	774

433	GGCN{20}CCC	57	29	0.82	775

434	GCAN{17}CGC	19	5	0.82	776

435	CGAN{11}ACG	9	1	0.81	777

436	CGCN{2}GGA	19	5	0.81	778

437	CTGN{5}CCC	79	45	0.8	779

438	TCCN{20}CCA	77	43	0.8	780

439	CCAN{2}GGG	59	30	0.8	781

440	CCGN{15}GCG	14	3	0.8	782

441	CCAN{5}GGG	69	38	0.79	783

442	CGGN{1}TGC	24	8	0.79	784

443	CCCN{14}GCG	21	6	0.79	785

444	CAGN{0}CCG	27	10	0.79	786

445	GCCN{9}TCC	60	31	0.78	787

446	AGGN{20}CGC	22	7	0.78	788

447	CCCN{6}GAC	42	19	0.77	789

448	CGGN{11}CCA	23	7	0.76	790

449	GGGN{14}CAC	57	29	0.75	791

450	GCAN{15}CGC	19	5	0.74	792

451	CGCN{2}ACA	20	6	0.74	793

452	ACCN{9}CCC	57	29	0.73	794

453	GCGN{9}CGC	20	3	0.73	795

454	CAGN{15}GCG	23	7	0.73	796

455	CCCN{18}GTC	45	21	0.72	797

456	GCGN{3}CCC	24	8	0.72	798

457	CGGN{11}GCC	23	8	0.72	799

458	CCCN{1}CGG	24	8	0.71	800

459	GCCN{4}CCA	70	38	0.71	801

460	CCCN{4}CCG	30	12	0.7	802

461	CGTN{2}GCA	21	6	0.7	803

462	AGCN{7}TCG	18	5	0.69	804

463	CCGN{15}GAA	20	6	0.69	805

464	ACCN{5}CCC	62	33	0.69	806

465	CGCN{14}GAG	19	5	0.68	807

466	CCCN{7}CGC	30	12	0.68	808

467	GAGN{12}CGC	21	6	0.68	809

468	GGCN{17}CCC	58	30	0.67	810

469	ACGN{11}CTC	21	7	0.65	811

470	ACAN{9}CGG	24	8	0.65	812

471	CTGN{7}CCC	82	47	0.65	813

472	CCCN{2}GCC	72	40	0.65	814

473	CGGN{2}GCA	24	8	0.64	815

474	CCCN{0}TGC	83	48	0.64	816

475	CGCN{7}ACC	18	5	0.63	817

476	GCAN{2}GCC	54	27	0.63	818

477	GCGN{8}CCA	20	6	0.63	819

478	AGCN{0}CGC	22	7	0.63	820

479	GCGN{2}GCA	18	5	0.63	821

480	CCGN{2}GTC	18	5	0.62	822

481	CCGN{3}ACA	21	7	0.62	823

482	ACGN{13}TGG	21	7	0.62	824

483	CCAN{8}CGC	23	8	0.62	825

484	CCGN{9}GGC	23	8	0.61	826

485	CCAN{5}CCG	25	9	0.61	827

486	AGGN{3}GGG	97	59	0.61	828

487	CAGN{2}GGC	78	45	0.61	829

488	CCCN{8}CAG	81	47	0.61	830

489	AGCN{5}CAG	80	46	0.6	831

490	CGGN{16}GCC	22	7	0.6	832

491	GCGN{15}CCC	23	8	0.6	833

492	CCCN{11}GCC	59	31	0.59	834

493	CGAN{2}ACG	9	1	0.59	835

494	CGGN{4}GCC	22	7	0.59	836

495	CACN{6}CGC	19	6	0.59	837

496	CGGN{5}ACG	11	2	0.59	838

497	CTGN{4}GCC *	66	36	0.59	839

498	GGGN{18}CGA	18	5	0.59	840

499	CCTN{8}CGC	22	7	0.59	841

500	GCCN{4}CCC	67	37	0.58	842

501	CGGN{10}GCC	22	7	0.58	843

502	GCCN{5}GGA	54	27	0.57	844

503	ACCN{7}GCG	15	4	0.57	845

504	CCCN{8}CGC	24	8	0.57	846

505	CAGN{5}CCC	77	44	0.56	847

506	CACN{14}GGA	63	34	0.56	848

507	CCCN{1}GCC	94	57	0.55	849

508	CCCN{5}AGC	67	37	0.55	850

509	GGCN{5}GGA	59	31	0.55	851

510	CGAN{17}GAG	19	6	0.55	852

511	CGCN{7}ACA	18	5	0.54	853

512	CCAN{13}CCC	87	52	0.54	854

513	CGGN{20}GGC	24	8	0.54	855

514	CCCN{17}GCC	58	30	0.53	856

515	CCTN{10}CCG	30	12	0.53	857

516	CCCN{8}CCG	27	10	0.53	858

517	CGCN{3}GAG	18	5	0.52	859

518	CGCN{7}AAG	17	5	0.51	860

519	CGGN{11}GGA	23	8	0.51	861

520	CCGN{15}CCG	15	4	0.51	862

521	CCCN{3}GCA	57	30	0.51	863

522	CGGN{2}CAG	24	8	0.5	864

523	AGGN{2}CCG	24	8	0.5	865

524	CCCN{4}CAC	69	38	0.5	866

525	GGAN{19}CCC	56	29	0.49	867

526	CCCN{8}CAC	68	38	0.49	868

527	ACCN{6}CCG	18	5	0.49	869

528	CCCN{6}GGC	54	28	0.49	870

529	CCCN{6}CCG	29	11	0.48	871

530	CGCN{14}GCC	26	9	0.47	872

531	CCGN{5}TCC	25	9	0.46	873

532	GCCN{6}GCC	55	28	0.46	874

533	CGGN{7}GGA	24	8	0.45	875

534	GGGN{6}GGA	87	52	0.44	876

535	GCCN{12}TCC	60	32	0.44	877

536	AGTN{16}CCG	17	5	0.44	878

537	GGCN{19}GCC	68	29	0.44	879

538	CCGN{3}CCG	22	7	0.44	880

539	CCCN{8}ACC	58	31	0.44	881

540	CAGN{15}GCC	77	44	0.44	882

541	CCCN{17}CGG	24	8	0.44	883

542	GCGN{1}CCA	22	7	0.44	884

543	CCCN{14}CAG	79	46	0.44	885

544	CCCN{8}CCC	89	53	0.44	886

545	ACAN{12}GCG	23	8	0.43	887

546	AGGN{4}CCG	23	8	0.43	888

547	CGCN{13}GCC	23	8	0.43	889

548	GAGN{2}CGC	23	8	0.42	890

549	CCCN{9}GCG	21	7	0.42	891

550	CGCN{17}ACA	17	5	0.42	892

551	GCGN{17}CCA	23	8	0.42	893

552	AAGN{18}CCG	20	6	0.42	894

553	CGCN{1}GGA	18	5	0.41	895

554	CCAN{1}CCC	90	54	0.41	896

555	CGTN{18}TGC	20	6	0.41	897

556	TCCN{14}CGA	17	5	0.41	898

557	CACN{5}GGG	56	29	0.4	899

558	CCGN{12}GCA	21	7	0.4	900

559	CTGN{6}CCC	77	44	0.4	901

560	CGGN{8}GGC	32	13	0.4	902

561	CCAN{11}GGG	68	38	0.4	903

562	ACGN{19}CAA	21	7	0.39	904

563	GGGN{20}CCC	72	31	0.39	905

564	CGCN{3}CAG	23	8	0.39	906

565	AGCN{17}GGG	58	31	0.37	907

566	CACN{20}CCG	21	7	0.37	908

567	ACGN{17}CAG	24	8	0.37	909

568	AGGN{1}CCC	60	32	0.37	910

569	CGTN{12}CAC	20	6	0.37	911

570	CGGN{9}GGC	23	8	0.37	912

571	CGCN{10}GCG	18	3	0.37	913

572	CCCN{6}CTC	80	47	0.36	914

573	CCGN{10}AGG	23	8	0.36	915

574	CCCN{18}CAG	79	46	0.36	916

575	AGCN{17}CCG	21	7	0.36	917

576	AGCN{9}GCG	18	5	0.36	918

577	CCAN{3}GGC	62	34	0.36	919

578	CCCN{11}GGC	57	30	0.35	920

579	ACGN{5}GCA	23	8	0.35	921

580	CCCN{14}CGG	23	8	0.35	922

581	CCCN{5}CCA	91	55	0.35	923

582	CCGN{1}AGG	22	7	0.34	924

583	GGGN{10}GAC	45	22	0.34	925

584	CGCN{15}CCA	20	6	0.34	926

585	CCTN{19}CGC	22	7	0.34	927

586	CGTN{3}CGC	10	2	0.33	928

587	AGCN{14}CCG	21	7	0.33	929

588	GGCN{2}CGA	17	5	0.33	930

589	CAGN{8}CCC	79	46	0.33	931

590	CCGN{2}GAC	16	4	0.33	932

591	AGCN{19}AGG	70	40	0.32	933

592	CCTN{4}GGC	64	35	0.32	934

593	CCGN{11}AGC	22	7	0.32	935

594	CACN{4}CGC	18	5	0.32	936

595	CCGN{1}CCC	30	12	0.31	937

596	CTGN{13}GGC	73	42	0.31	938

597	CGCN{16}ACC	15	4	0.31	939

598	CACN{18}CAG	79	46	0.31	940

599	GGCN{8}GCC	68	29	0.29	941

600	GGGN{15}GGA	78	46	0.29	942

601	CCGN{16}GCC	22	7	0.29	943

602	CCGN{20}ACC	18	5	0.29	944

603	CGAN{7}CCC	17	5	0.28	945

604	CCGN{6}CTC	23	8	0.28	946

605	CGGN{10}CTC	22	7	0.28	947

606	CAGN{16}CGC	23	8	0.28	948

607	CCAN{3}AGG	77	45	0.27	949

608	GCCN{18}GCC	52	27	0.27	950

609	CGCN{18}GGA	19	6	0.26	951

610	CCGN{20}GGC	22	7	0.26	952

611	ACAN{10}GCG	17	5	0.26	953

612	CGGN{5}CCC	25	9	0.25	954

613	CCCN{7}TCC	75	43	0.25	955

614	ACGN{10}CGC	10	2	0.25	956

615	CCCN{3}TCC	81	48	0.25	957

616	CCGN{8}CGG	20	3	0.24	958

617	CCAN{15}CGG	22	7	0.24	959

618	CCGN{6}CCG	17	5	0.24	960

619	CAGN{3}GCG	25	9	0.24	961

620	GAGN{1}CCC	62	34	0.24	962

621	CCGN{18}TGC	22	7	0.23	963

622	CCCN{7}CCA	85	51	0.23	964

623	CGGN{3}CCA	24	9	0.23	965

624	ACGN{1}CCC	18	5	0.23	966

625	CGGN{13}TGA	21	7	0.22	967

626	CTCN{6}GGC	53	28	0.22	968

627	GCGN{2}GAC	15	4	0.22	969

628	GGGN{11}ACC	49	25	0.22	970

629	CGCN{4}GGA	17	5	0.22	971

630	CCCN{11}CCG	27	10	0.22	972

631	CCGN{19}GCA	20	6	0.22	973

632	GCGN{0}GCA	20	6	0.21	974

633	AGAN{7}CCC	61	33	0.21	975

634	CGGN{2}CCA	21	7	0.21	976

635	CCCN{7}CCC	89	54	0.21	977

636	ACCN{4}GCG	15	4	0.2	978

637	CCTN{15}CGC	20	6	0.2	979

638	AGCN{9}GTC	44	21	0.2	980

639	CCCN{18}CTC	74	43	0.2	981

640	CGCN{18}CGA	9	1	0.19	982

641	CCCN{15}GCC	62	34	0.18	983

642	ACCN{11}GGC	45	22	0.18	984

643	AGGN{15}CGC	29	12	0.18	985

644	GCGN{0}CCA	27	10	0.18	986

645	GCGN{9}AGC	18	5	0.17	987

646	GGGN{18}GCA	59	32	0.17	988

647	CCCN{17}CAG	77	45	0.17	989

648	CCAN{8}CGG	22	8	0.16	990

649	CCGN{10}GGC	21	7	0.16	991

650	GCAN{0}GCC	76	44	0.16	992

651	CAGN{2}CGC	20	6	0.16	993

652	CGCN{8}GGC	19	6	0.16	994

653	CTGN{17}GGC	65	36	0.16	995

654	GGGN{14}ACC	46	23	0.16	996

655	CCGN{1}TGC	20	6	0.16	997

656	CAGN{8}CGC	22	8	0.15	998

657	AAGN{11}CGC	17	5	0.15	999

658	CCGN{6}TCC	22	8	0.14	1000

659	CCAN{18}CCC	72	42	0.14	1001

660	CCAN{0}CCC	84	51	0.14	1002

661	GAGN{6}CCC	53	28	0.14	1003

662	AGCN{20}GGC	52	27	0.14	1004

663	CAGN{0}CGC	21	7	0.14	1005

664	CCGN{12}CTC	22	8	0.14	1006

665	CGCN{15}ACG	9	1	0.13	1007

666	GGCN{17}CGA	15	4	0.13	1008

667	CCGN{16}AAG	19	6	0.13	1009

668	CGCN{14}TCC	19	6	0.12	1010

669	AGGN{7}CGC	20	7	0.12	1011

670	CGGN{7}CCC	22	8	0.12	1012

671	CGCN{4}GCC	34	15	0.12	1013

672	CGAN{6}CCC	17	5	0.12	1014

673	CCCN{19}GGA	60	33	0.11	1015

674	CCCN{16}GCG	28	11	0.11	1016

675	CCAN{7}CGC	20	7	0.11	1017

676	CCCN{6}GCC	80	48	0.11	1018

677	GCCN{14}TCC	55	29	0.11	1019

678	AGGN{14}GCC	64	36	0.1	1020

679	CGCN{11}GCC	20	7	0.1	1021

680	TCCN{0}GCA	17	5	0.09	1022

681	GCGN{8}CCC	27	11	0.09	1023

682	CCAN{11}GCG	19	6	0.09	1024

683	CACN{4}GGG	51	26	0.09	1025

684	CGGN{7}TCC	20	7	0.09	1026

685	GCGN{5}GCC	20	7	0.09	1027

686	ACGN{12}CAG	26	10	0.09	1028

687	CCGN{19}CGC	14	4	0.08	1029

688	CGGN{8}TGC	18	5	0.08	1030

689	CCCN{1}GAG	65	37	0.07	1031

690	GCGN{19}TGA	18	6	0.07	1032

691	GGCN{15}GCC	70	31	0.07	1033

692	CCGN{7}CCC	27	11	0.07	1034

693	ACAN{19}CCC	63	35	0.07	1035

694	ACCN{16}GGG	47	24	0.07	1036

695	AGAN{1}GGC	64	36	0.07	1037

696	GGGN{17}TGA	64	36	0.06	1038

697	CAGN{5}GGG	83	50	0.06	1039

698	GCCN{13}CGC	22	8	0.06	1040

699	GCGN{7}GGA	19	6	0.06	1041

700	CAGN{14}CCA	94	58	0.06	1042

701	CCGN{4}GTC	16	4	0.06	1043

702	CCCN{13}CGC	22	8	0.06	1044

703	GCGN{14}ACC	15	4	0.05	1045

704	CAGN{20}GGG	81	49	0.05	1046

705	CCGN{4}CCC	27	11	0.05	1047

706	CGCN{5}GGC	18	6	0.05	1048

707	CCTN{6}GGC	57	31	0.05	1049

708	AGGN{3}GGC	67	38	0.05	1050

709	CGGN{11}CGC	14	4	0.05	1051

710	CTGN{18}GGA	77	46	0.04	1052

711	CACN{17}CCA	74	43	0.04	1053

712	CGGN{3}GAG	22	8	0.04	1054

713	CCCN{9}CCA	82	49	0.03	1055

714	CCCN{1}ACG	18	6	0.03	1056

715	CAGN{1}GCC	72	42	0.03	1057

716	AGGN{6}CCG	23	8	0.03	1058

717	AGCN{9}GGG	57	31	0.03	1059

718	CCCN{7}GGC	54	29	0.02	1060

719	CCTN{13}CCC	88	54	0.02	1061

720	CCGN{19}TTC	20	7	0.02	1062

721	CCCN{7}CCG	27	11	0.02	1063

722	CGAN{6}GGC	17	5	0.01	1064

723	CGGN{4}CTC	21	7	0.01	1065

724	CGGN{0}CGC	13	3	0.01	1066

725	CCTN{13}ACG	19	6	0.01	1067

726	GGGN{6}CAC	53	28	0.01	1068

727	CCCN{16}CGC	21	7	0.01	1069

728	CCCN{10}CTC	76	45	0	1070

729	CCCN{0}CAG	92	57	0	1071

730	GCCN{5}CCC	65	37	0	1072

TABLE 8

Candidate STAR elements tested by Linear Discriminant Analysis
(SEQ ID NOS: 66-84)

SEQ ID NO:	Candidate STAR	Location¹	Length

66	T2 F	20q13.33	~2800
67	T2 R	6q14.1	~2800
68	T3 F	15q12	~2900
69	T3 R	7q31.2	~2900
70	T5 F	9q34.13	ND²
71	T5 R	9q34.13	ND
72	T7	22q12.3	~1200
73	T9 F	21q22.2	~1600
74	T9 R	22q11.22	~1600
75	T10 F	7q22.2	~1300
76	T10 R	6q14.1	~1300
77	T11 F	17q23.3	~2000
78	T11 R	16q23.1	~2000
79	T12	4p15.1	~2100
80	T13 F	20p13	~1700
81	T13 R	1p13.3	~1700
82	T14 R	11q25	~1500
83	T17	2q31.3	ND
84	T18	2q31.1	ND

¹Chromosomal location is determined by BLAT search of DNA sequence data from the STAR elements against the human genome database. The location is given according to standard nomenclature referring to the cytogenetic ideogram of each chromosome; e.g., 1p2.3 is the third cytogenetic sub-band of the second cytogenetic band of the short arm of chromosome 1 (http://www.ncbi.nlm.nih.gov/Class/MLACourse/Genetics/chrombanding.html). F, forward sequencing reaction result; R, reverse sequencing reaction result. When the forward and reverse sequencing results mapped to different genomic locations, each sequence was extended to the full length of the original clone (as determined by restriction mapping) based on sequence information from the human genome database.
²ND: Not Determined.

TABLE 9

Arabidopsis STAR elements of the invention, including
chromosome location and length (SEQ ID NOS: 85-119)

	STAR	Chromosome	Length, kb	SEQ ID NO:

A1	I	1.2	85
A2	I	0.9	86
A3	I	0.9	87
A4	I	0.8	88
A5	I	1.3	89
A6	I	1.4	90
A7	II	1.2	91
A8	II	0.8	92
A9	II	0.9	93
A10	II	1.7	94
A11	II	1.9	95
A12	II	1.4	96
A13	II	1.2	97
A14	II	2.1	98
A15	II	1.4	99
A16	II	0.7	100
A17	II	1.5	101
A18	III	1.5	102
A19	III	0.7	103
A20	III	2.0	104
A21	IV	1.8	105
A22	IV	0.8	106
A23	IV	0.6	107
A24	IV	0.5	108
A25	V	0.9	109
A26	V	1.9	110
A27	V	1.1	111
A28	V	1.6	112
A29	V	0.9	113
A30	V	2.0	114
A31	V	2.0	115
A32	V	1.3	116
A33	V	0.9	117
A34	I	0.9	118
A35	II	1.1	119

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Claims

1. A method for producing a proteinaceous molecule in a cell comprising:

providing a cell selected from the group consisting of: a cell having an adenovirus Early Region 1 (E1) sequence, a HuNS-1 myeloma cell, a 293 cell, a CHO cell, a Vero cell, a WERI-Rb-1 retinoblastoma cell, a BHK cell, a non-secreting mouse myeloma Sp2/0-Ag 14 cell, a non-secreting mouse myeloma NSO cell, and an NCI-H295R adrenal gland carcinoma cell;

wherein said cell comprises an anti-repressor activity sequence operably linked to a nucleic acid sequence encoding a heterologous proteinaceous molecule, wherein said anti-repressor activity sequence comprises SEQ ID NO:44;

expressing the proteinaceous molecule in said cell; and

isolating said proteinaceous molecule.

2. The method of claim 1, wherein said anti-repressor activity sequence is SEQ ID NO:44.

3. The method of claim 1, wherein said cell comprises an adenovirus Early Region 1 (E1) sequence.

4. The method of claim 1, wherein said proteinaceous molecule is secreted by said cell.

5. The method of claim 2, wherein said proteinaceous molecule is secreted by said cell.

6. The method of claim 1, wherein said cell comprises a plurality of the anti-repressor activity sequence operably linked to said nucleic acid sequence encoding the heterologous proteinaceous molecule.

7. The method of claim 6, wherein at least one anti-repressor activity sequence is positioned 5′ of the sequence encoding the proteinaceous molecule and at least one anti-repressor activity sequence is positioned 3′ of the sequence encoding the proteinaceous molecule.

8. The method of claim 1, wherein said cell is a CHO cell.

9. The method of claim 6, wherein said cell is a CHO cell.

10. The method of claim 7, wherein said cell is a CHO cell.

11. A recombinant host cell line, comprising:

a cell selected from the group consisting of: a cell line comprising an adenovirus Early Region 1 (E1) sequence, a HuNS-1 myeloma cell line, a 293 cell line, a CHO cell line, a Vero cell line, a WERI-Rb-1 retinoblastoma cell line, a BHK cell line, a non-secreting mouse myeloma Sp2/0-Ag 14 cell line, a non-secreting mouse myeloma NSO cell line, and an NCI-H295R adrenal gland carcinoma cell line;

said cell comprising an anti-repressor activity sequence operably linked to a nucleic acid sequence encoding a heterologous proteinaceous molecule, wherein said anti-repressor activity sequence comprises SEQ ID NO:44.

12. The cell line of claim 11, wherein said anti-repressor activity sequence is SEQ ID NO:44.

13. The cell line of claim 11, wherein said cell line comprises an adenovirus Early Region 1 sequence.

14. The cell line of claim 11, wherein said cell comprises a plurality of the anti-repressor activity sequence operably linked to said nucleic acid sequence encoding the heterologous proteinaceous molecule.

15. The cell line of claim 11, wherein at least one anti-repressor activity sequence is positioned 5′ of the sequence encoding the proteinaceous molecule and at least one anti-repressor activity sequence is positioned 3′ of the sequence encoding the proteinaceous molecule.

16. The cell line of claim 11, wherein said cell line is a CHO cell line.

17. The cell line of claim 14, wherein said cell line is a CHO cell line.

18. The cell line of claim 15, wherein said cell line is a CHO cell line.